Apparatus and method for inferring the origin of chromosome segments in a pedigree

A chromosome and genealogy technology, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problems of missing sample data information, affecting the coherence and integrity of the genealogy, and no effective methods available, etc., to achieve simple operation, good compatibility

Active Publication Date: 2017-09-26
BEIJING NOVOGENE TECH CO LTD
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Problems solved by technology

[0003] Different from higher mammal groups such as humans, for botanical research, in the field of genetics and breeding, selfing is a routine means of breeding, resulting in many pedigree groups produced by selfing; in addition, due to some reasons, a large number of samples Data information is missing or the complete pedigree structure information cannot be obtained, which affects the coherence and integrity of the pedigree
Therefore, so far, there is no effective method available for the reconstruction of the genetic relationship at the DNA molecular level for the above-mentioned complex pedigree

Method used

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  • Apparatus and method for inferring the origin of chromosome segments in a pedigree
  • Apparatus and method for inferring the origin of chromosome segments in a pedigree
  • Apparatus and method for inferring the origin of chromosome segments in a pedigree

Examples

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Embodiment 1

[0044] A rice pedigree, consisting of eight samples of A, B, C, D, E, F, G and H, currently only know the local pedigree of three samples, such as figure 2 As shown, that is, A and B are the parents of C; A and D are the parents of E; E and F are the parents of G; E and G are the parents of H.

[0045] according to image 3 As shown, by using the IBDseq algorithm to compare the chromosomes of the above 8 samples in pairs, through the comparison of A and B, the same chromosome segment between A and B is found; then A and C are compared to find A and C Between the same chromosome segment, followed by A and D, A and E, and so on, until G and H, to find the same chromosome segment between each two samples in 8 samples; then the whole genome of rice Genetic segments are divided to obtain a plurality of different types of genetic segments; and then according to the types of each genetic segment, the above-mentioned 8 samples are grouped according to the type of each genetic segmen...

Embodiment 2

[0059] The pedigree samples of Example 2 and the steps before obtaining different grouped samples are the same as those in Example 1, and the origin of the fifth genetic segment of each sample is inferred, the difference is that the retrospective analysis method used is different, The backtracking analysis in Example 2 is inferred by recording the path experienced by each sample in the previous step of the search, and the next step of the search path does not need to return to the sample at the starting point, but only needs to return to the bifurcation point and continue to search for the path that has not been experienced. The specific analysis process is as Figure 5 said, where:

[0060] A is the ancestral sample in the pedigree, its theoretical backtracking path is the same as the actual backtracking path, and the type of its genetic segment is still the A sample itself; similarly,

[0061] The genetic segment type of the B sample is also the B sample itself;

[0062] T...

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Abstract

The invention discloses a device and method for inferring the origin of chromosome segments in pedigree. The method includes the following steps: pairwise chromosome comparison of all samples in the pedigree to obtain the same chromosome segment information between the two pairs; dividing the whole genome into multiple different types of chromosome segments according to the same chromosome segment information between the pairwise Genetic segment; divide all samples into multiple genetic segment sample groups according to the type of genetic segment; retrospectively analyze the origin of each genetic segment in each sample based on the known local genetic relationship between every three samples in the pedigree , to obtain all possible genetic paths of each genetic segment of each sample, and record the last sample in each genetic path as the end point sample; according to the order of the end point samples and the samples in the pedigree, it is inferred that the sample with the highest position is each The ancestral sample of the genetic segment of each sample is used to complete the inference of the source of the chromosome segment in the pedigree. This method does not require complete pedigree structure information and has good compatibility.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a device and method for inferring the origin of chromosome segments in a pedigree. Background technique [0002] With the development of next-generation sequencing technology, the detection of IBS (Identity by state) and IBD (Identity by decent) at the genome-wide level has been widely used in the field of genetic relationship analysis of samples within a pedigree. At present, IBS and IBD detection methods based on genome-wide variation detection are relatively mature, such as widely used Plink, Beagle fastIBD, GERMLINE, etc., and newly published Beagle refinedIBD, IBDseq, HapFABIA, etc. However, these methods are mainly used in the research of higher mammals such as humans, such as studying the genetic relationship of different races of humans based on pedigree relationship and IBD data, so as to infer human evolution history; or inferring the pedigree structure based on IBD data, a...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/18
Inventor 闫军张彦丽侯凌燕吴俊
Owner BEIJING NOVOGENE TECH CO LTD
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