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Device and method for genealogy reestablishing on molecular level

A technology of molecular level and genealogy, which is applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problem that the genealogy at the plant molecular level cannot be reconstructed, and achieve the effect of fast genealogy reconstruction and simple operation

Active Publication Date: 2014-11-05
BEIJING NOVOGENE TECH CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] The present invention aims to provide a device and method for pedigree reconstruction at the molecular level, so as to solve the defect that the pedigree at the plant molecular level cannot be reconstructed in the prior art

Method used

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  • Device and method for genealogy reestablishing on molecular level
  • Device and method for genealogy reestablishing on molecular level
  • Device and method for genealogy reestablishing on molecular level

Examples

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Embodiment 1

[0066] The object of embodiment 1 is an orthologous pedigree composed of 7 samples. It is known that sample A3 is the descendant generation of samples A1 and A2, sample A3 and sample A4 are the parent generation of A5, and the descendant generation samples of samples A5 and A6 For A7, the high-throughput sequencing data of 7 samples in the pedigree all exist, as follows figure 1 The shown pipeline reconstructs this family tree at the molecular level:

[0067] The IBDseq algorithm is used to compare the IBD block information of the 7 samples in the pedigree, such as figure 2 As shown, sample A1 and sample A2 are subjected to IBD block detection to obtain the chromosome information shared between sample A1 and sample A2; similarly, A1 and sample A3 are then subjected to IBD block detection to obtain sample A1 and sample A3 Chromosome information shared between, as mentioned above, A1 and A4, A1 and A5, A1 and A6, A1 and A7, A2 and A3, A2 and A4, ... and A6 and A7, that is, all...

Embodiment 2

[0073] The object of embodiment 2 is a pedigree composed of 9 samples belonging to different orthologous pedigrees. It is known that sample A3 is the offspring generation of samples A1 and A2, sample A3 and sample B3 are the parent generation of A5, and sample A5 The offspring sample of A6 and A6 is A7, and the parents of sample B3 are B1 and B2; the high-throughput sequencing data of sample A6 is missing. follow below image 3 The shown pipeline reconstructs this family tree at the molecular level:

[0074] The steps of carrying out IBD block detection, genetic block division and grouping of 9 samples according to genetic block types are the same as in Example 1 for the 9 samples in the pedigree;

[0075] In order to ensure the continuity of the pedigree and the integrity of the data, it is necessary to infer the most likely genetic block type of sample A6 with missing data according to the genetic block type of close relatives:

[0076] When the genetic block types of the ...

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Abstract

The invention discloses a device and method for genealogy reestablishing on the molecular level. The method comprises the following steps that all samples in genealogy are subjected to chromosome comparison in a pairing mode, and identical chromosome region information obtained by pairing comparison in all the samples is obtained; according to the identical chromosome region information obtained by pairing comparison in all the samples, a whole genome is subjected to heredity region division, and a plurality of heredity regions of different types are obtained; according to the different types of the heredity regions, all the samples in the genealogy are subjected to heredity region group division, and a plurality of heredity region sample groups are obtained; according to the known genetic relationship between the samples in the genealogy, the heredity sources of the heredity regions of each sample in each heredity region sample group are subjected to inference, and the heredity sources of the heredity regions of all the samples in the genealogy are obtained; and accordingly genealogy reestablishing on the molecular level is completed. The method has the obvious advantages of being precise, complete in function, easy to operate and good in compatibility.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a device and method for genealogy reconstruction at the molecular level. 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, and then pe...

Claims

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Application Information

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IPC IPC(8): G06F19/16
Inventor 闫军张彦丽吴俊张莹莹吴成琼
Owner BEIJING NOVOGENE TECH CO LTD
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