RECONSTRUCTING A PRECURSORY INHERITANCE DATASET
Disclosed is a method for reconstructing a precursory genome using cognates' genotype data. The method includes receiving a plurality of data instances from a plurality of cognates, each data instance corresponding to one of the cognates. The method includes phasing each data instance to generate a pair of phased data segments for each cognate of the plurality of cognates and comparing the phased data segments of the plurality of cognates to identify, for each cognate, one of the phased data segments that is inherited from a target parent. The method further includes extracting, for each cognate, the phased data segment that is inherited from the target parent to form a set of cognate phased data segments that are inherited from the target parent. The method includes identifying data exchange breakpoints in the set of cognate phased data segments and reconstructing a pair of precursory phased data segments.
1 . A computer-implemented method for reconstructing precursory data segments, the computer-implemented method comprising:
receiving a plurality of data instances from a plurality of cognates, each data instance corresponding to one of the cognates;
phasing each data instance to generate a pair of phased data segments for each cognate of the plurality of cognates;
comparing the phased data segments of the plurality of cognates to identify, for each cognate, one of the phased data segments that is inherited from a target precursor;
extracting, for each cognate, the phased data segment that is inherited from the target precursor to form a set of cognate phased data segments that are inherited from the target precursor;
identifying data exchange breakpoints in the set of cognate phased data segments, wherein identifying the data exchange breakpoints comprises identifying data mismatch locations among the cognate phased data segments; and
reconstructing a pair of precursory phased data segments based on the identified data exchange breakpoints.
2 . The computer-implemented method of claim 1 , wherein the plurality of data instances is associated with a plurality of data storage locations from the plurality of cognates, and phasing each data instance comprises:
generating a pair of phased data segments for each cognate for each of the plurality of data storage locations.
3 . The computer-implemented method of claim 2 , wherein comparing the phased data segments of the plurality of cognates comprise:
comparing the phased data segments of the plurality of cognates that are associated with a same data storage location; and
identifying, for each cognate and for each data storage location, one of the pair of phased data segments that is inherited from one precursor of the cognates and the other of the pair of phased data segments is inherited from the other precursor of the cognates.
4 . The computer-implemented method of claim 1 , wherein identifying data exchange breakpoints in the set of cognate phased data segments comprises:
at each data mismatch location, determining a data exchange breakpoint using a voting process, wherein a majority of the cognate phased data segments in the voting process does not have the data exchange breakpoint, and a minority of the cognate phased data segments in the voting process has the data exchange breakpoint where a corresponding phased data segment changes from being associated with one ultra-precursor's phased data segment to another ultra-precursor's phased data segment.
5 . The computer-implemented method of claim 1 , wherein reconstructing a pair of precursory phased data segments based on the identified data exchange breakpoints comprises:
rearranging the set of cognate phased data segments at the identified data exchange breakpoints.
6 . The computer-implemented method of claim 1 , wherein reconstructing a pair of precursory phased data segments based on the identified data exchange breakpoints comprises:
identifying one or more portions of the set of cognate phased data segments based on the identified data exchange breakpoints; and
assigning each of the one or more portions of the set of cognate phased data segments to a precursor of the target precursor.
7 . The computer-implemented method of claim 6 , further comprising:
grouping the one or more portions of the set of cognate phased data segments according to the assigned precursor of the target precursor; and
rearranging the grouped portions of the cognate phased data segments to reconstruct a precursory phased data segment that is inherited from the assigned precursor of the target precursor.
8 . The computer-implemented method of claim 1 , wherein at least two of the plurality of cognates are full cognates who share same two precursors.
9 . A computer-readable storage medium having stored thereon computer-executable instructions that, when executed by one or more processors, cause the one or more processors to perform operations, comprising:
receiving a plurality of data instances from a plurality of cognates, each data instance corresponding to one of the cognates;
phasing each data instance to generate a pair of phased data segments for each cognate of the plurality of cognates;
comparing the phased data segments of the plurality of cognates to identify, for each cognate, one of the phased data segments that is inherited from a target precursor;
extracting, for each cognate, the phased data segment that is inherited from the target precursor to form a set of cognate phased data segments that are inherited from the target precursor;
identifying data exchange breakpoints in the set of cognate phased data segments, wherein identifying the data exchange breakpoints comprises identifying data mismatch locations among the cognate phased data segments; and
reconstructing a pair of precursory phased data segments based on the identified data exchange breakpoints.
10 . The computer-readable storage medium of claim 9 , wherein the plurality of data instances is associated with a plurality of data storage locations from the plurality of cognates, and phasing each data instance comprises:
generating a pair of phased data segments for each cognate for each of the plurality of data storage locations.
11 . The computer-readable storage medium of claim 10 , wherein comparing the phased data segments of the plurality of cognates comprise:
comparing the phased data segments of the plurality of cognates that are associated with a same data storage location; and
identifying, for each cognate and for each data storage location, one of the pair of phased data segments that is inherited from one precursor of the cognates and the other of the pair of phased data segments is inherited from the other precursor of the cognates.
12 . The computer-readable storage medium of claim 9 , wherein identifying data exchange breakpoints in the set of cognate phased data segments comprises:
at each data mismatch location, determining a data exchange breakpoint using a voting process, wherein a majority of the cognate phased data segments in the voting process does not have the data exchange breakpoint, and a minority of the cognate phased data segments in the voting process has the data exchange breakpoint where a corresponding phased data segment changes from being associated with one ultra-precursor's phased data segment to another ultra-precursor's phased data segment.
13 . The computer-readable storage medium of claim 9 , wherein reconstructing a pair of precursory phased data segments based on the identified data exchange breakpoints comprises:
rearranging the set of cognate phased data segments at the identified data exchange breakpoints.
14 . The computer-readable storage medium of claim 9 , wherein reconstructing a pair of precursory phased data segments based on the identified data exchange breakpoints comprises:
identifying one or more portions of the set of cognate phased data segments based on the identified data exchange breakpoints; and
assigning each of the one or more portions of the set of cognate phased data segments to a precursor of the target precursor.
15 . The computer-readable storage medium of claim 14 , wherein the operations further comprise:
grouping the one or more portions of the set of cognate phased data segments according to the assigned precursor of the target precursor; and
rearranging the grouped portions of the cognate phased data segments to reconstruct a precursory phased data segment that is inherited from the assigned precursor of the target precursor.
16 . A computer system, comprising:
one or more processors; and
a hardware storage device having stored thereon computer-executable instructions that, when executed by the one or more processors, causes the computer system to perform operations, comprising:
receiving a plurality of data instances from a plurality of cognates, each data instance corresponding to one of the cognates;
phasing each data instance to generate a pair of phased data segments for each cognate of the plurality of cognates;
comparing the phased data segments of the plurality of cognates to identify, for each cognate, one of the phased data segments that is inherited from a target precursor;
extracting, for each cognate, the phased data segment that is inherited from the target precursor to form a set of cognate phased data segments that are inherited from the target precursor;
identifying data exchange breakpoints in the set of cognate phased data segments, wherein identifying the data exchange breakpoints comprises identifying data mismatch locations among the cognate phased data segments; and
reconstructing a pair of precursory phased data segments based on the identified data exchange breakpoints.
17 . The computer system of claim 16 , wherein the plurality of data instances is associated with a plurality of data storage locations from the plurality of cognates, and phasing each data instance comprises:
generating a pair of phased data segments for each cognate for each of the plurality of data storage locations.
18 . The computer system of claim 17 , wherein comparing the phased data segments of the plurality of cognates comprise:
comparing the phased data segments of the plurality of cognates that are associated with a same data storage location; and
identifying, for each cognate and for each data storage location, one of the pair of phased data segments that is inherited from one precursor of the cognates and the other of the pair of phased data segments is inherited from the other precursor of the cognates.
19 . The computer system of claim 16 , wherein identifying data exchange breakpoints in the set of cognate phased data segments comprises:
at each data mismatch location, determining a data exchange breakpoint using a voting process, wherein a majority of the cognate phased data segments in the voting process does not have the data exchange breakpoint, and a minority of the cognate phased data segments in the voting process has the data exchange breakpoint where a corresponding phased data segment changes from being associated with one ultra-precursor's phased data segment to another ultra-precursor's phased data segment; and
rearranging the set of cognate phased data segments at the identified data exchange breakpoints.
20 . The computer system of claim 16 , wherein reconstructing a pair of precursory phased data segments based on the identified data exchange breakpoints comprises:
identifying one or more portions of the set of cognate phased data segments based on the identified data exchange breakpoints;
assigning each of the one or more portions of the set of cognate phased data segments to a precursor of the target precursor;
grouping the one or more portions of the set of cognate phased data segments
according to the assigned precursor of the target precursor; and
rearranging the grouped portions of the cognate phased data segments to reconstruct a precursory phased data segment that is inherited from the assigned precursor of the target precursor.