Parallel Bitwise Determination of Origin
Inferring a characteristic of an individual is disclosed. An indication that a first user and a second user have at least one shared chromosomal segment is received. Information about the second user is obtained. A characteristic of the first user is inferred based at least in part on the information about the second user.
1 . A system comprising:
two or more processors;
persistent memory containing program instructions that, when executed by the two or more processors cause the system to perform operations including:
encoding, in a plurality of bitwise arrays, respective zygosity states of markers for a plurality of individuals, wherein lengths of the bitwise arrays match a word length of the two or more processors;
identifying, in parallel by the two or more processors and using bitwise operations on the plurality of bitwise arrays, identical-by-descent sections each of at least a minimum length that a target individual shares with a subset of individuals from the plurality of individuals;
obtaining, from one or more databases, respective birthplace information for the subset of individuals;
based on the respective birthplace information for the subset of individuals, estimating respective origins of each of the identical-by-descent sections to be countries, geographical regions, or ethnicities; and
causing, on a graphical user interface, display of the identical-by-descent sections arranged within their respective chromosomes and colored to indicate their respective origins.
2 . The system of claim 1 , wherein the respective birthplace information indicates that at least some of the subset of individuals have two or more grandparents who were born in a country, born in a geographical region, or had an ethnicity indicating the respective origins.
3 . The system of claim 1 , wherein the identical-by-descent sections arranged within their respective chromosomes are presented in a karyotype view.
4 . The system of claim 1 , wherein the identical-by-descent sections are identified based on their containing common markers.
5 . The system of claim 1 , wherein the identical-by-descent sections are bounded by opposite homozygous calls.
6 . The system of claim 1 , wherein an origin of at least one of the identical-by-descent sections comprises two or more different countries, geographical regions, or ethnicities.
7 . The system of claim 1 , wherein the target individual and at least one of the subset of individuals were previously unknown to be related before the sharing of the identical-by-descent sections was determined.
8 . The system of claim 1 , wherein the respective origins are also displayed on the graphical user interface as a table of countries.
9 . The system of claim 1 , wherein the respective origins are also displayed on the graphical user interface as a pie chart of countries.
10 . The system of claim 1 , wherein the respective origins are also displayed on the graphical user interface as a map of countries.
11 . The system of claim 1 , the operations further comprising:
receiving an indication that a second target individual has a known degree of familial relationship to the target individual; and
determining, based on the respective origins estimated for the identical-by-descent sections of the target individual, an origin of the second target individual.
12 . A computer-implemented method comprising:
encoding, in a plurality of bitwise arrays, respective zygosity states of markers for a plurality of individuals, wherein lengths of the bitwise arrays match a word length of two or more processors;
identifying, in parallel by the two or more processors and using bitwise operations on the plurality of bitwise arrays, identical-by-descent sections each of at least a minimum length that a target individual shares with a subset of individuals from the plurality of individuals;
obtaining, from one or more databases, respective birthplace information for the subset of individuals;
based on the respective birthplace information for the subset of individuals, estimating respective origins of each of the identical-by-descent sections to be countries, geographical regions, or ethnicities; and
causing, on a graphical user interface, display of the identical-by-descent sections arranged within their respective chromosomes and colored to indicate their respective origins.
13 . The computer-implemented method of claim 12 , wherein the respective birthplace information indicates that at least some of the subset of individuals have two or more grandparents who were born in a country, born in a geographical region, or had an ethnicity indicating the respective origins.
14 . The computer-implemented method of claim 12 , wherein the identical-by-descent sections are identified based on their containing common markers.
15 . The computer-implemented method of claim 12 , wherein the identical-by-descent sections are bounded by opposite homozygous calls.
16 . The computer-implemented method of claim 12 , wherein an origin of at least one of the identical-by-descent sections comprises two or more different countries, geographical regions, or ethnicities.
17 . The computer-implemented method of claim 12 , wherein the target individual and at least one of the subset of individuals were previously unknown to be related before the sharing of the identical-by-descent sections was determined.
18 . The computer-implemented method of claim 12 , wherein the respective origins are also displayed on the graphical user interface as a table, pie chart, or map of countries.
19 . The computer-implemented method of claim 12 , further comprising:
receiving an indication that a second target individual has a known degree of familial relationship to the target individual; and
determining, based on the respective origins estimated for the identical-by-descent sections of the target individual, an origin of the second target individual.
20 . A system comprising:
two or more processors;
persistent memory containing program instructions that, when executed by the two or more processors cause the system to perform operations including:
determining, in parallel by the two or more processors and using bitwise operations on respective zygosity states of markers, that a target individual shares identical-by-descent segments each of at least a minimum length with a plurality of other individuals;
obtaining, from one or more databases, respective birthplace information of the other individuals;
based on the respective birthplace information of the other individuals, estimating respective origins of each of the identical-by-descent segments to be countries, geographical regions, or ethnicities; and
causing, on a graphical user interface, display of the identical-by-descent segments colored to indicate their respective origins.