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Genetic map construction method and device, haplotype analytical method and device

A genetic map and construction method technology, applied in sequence analysis, biochemical cleaning equipment, biochemical equipment and methods, etc., can solve problems such as incompleteness, one-sided genetic map, and restrictions on the construction process of human genetic map

Active Publication Date: 2013-03-06
TIANJIN MEDICAL LAB BGI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0003] However, the current traditional method of genetic map construction cannot be well applied to humans
Since the construction of the genetic map is based on the statistical analysis of the random distribution of homologous recombination events generated in meiosis to offspring individuals, it is necessary to select a large number of individuals in each generation for research, and mammals lack a large number of progeny for composition. It directly limits the construction process of the human genetic spectrum, because it is difficult to select such a large family to meet the conditions of statistical randomness for research
N.ARNHEIM, H.LI, etc. used single sperm to construct a genetic map (Genetic mapping by single sperm typing, Animal Genetics 1991, 22, 105-115), which solved the problem of sample selection, but there are still great limitations
The method used in this paper can only amplify some known genes for subsequent analysis. It not only depends on the effect of primers, but also can’t do anything about unknown genes and fragments that are not easy to amplify. Therefore, the genetic map obtained by this method is relatively one-sided. Complete

Method used

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  • Genetic map construction method and device, haplotype analytical method and device
  • Genetic map construction method and device, haplotype analytical method and device
  • Genetic map construction method and device, haplotype analytical method and device

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0119] Example 1: Construction of recombination map and genetic map by single sperm sequencing

[0120] 1.1 List of reagents and instruments

[0121] Table 1 Reagents stored at -20°C

[0122]

[0123]

[0124] Table 2 Reagents stored at 4°C

[0125]

[0126] Table 3 Reagents stored at room temperature (RT)

[0127]

[0128] Table 4 Common Consumables and Instruments

[0129]

[0130] 1X PBS solution preparation:

[0131] Weigh the following reagents, put them into a 1L beaker, and add 800mL of deionized water.

[0132]

[0133] Adjust the pH value to 7.4, add water to make up to 1L, store at 4°C after high-temperature and high-pressure sterilization, and add 15mg / ml BSA before use.

[0134] ALB solution preparation:

[0135] Weigh 0.02244g of KOH solid, put it into a 2ml centrifuge tube, add 2ml of ultrapure water, 101μl of DTT solution (1M), and mix evenly by inversion. In the ultra-clean workbench, filter with a 0.2 μm pore size filter. Immediatel...

Embodiment 2

[0211] Example 2: Single sperm sequencing to find recombination hot spots and analysis of haplotypes

[0212] The recombination map and genetic map were obtained according to the steps in Example 1.

[0213] Observe to find out the region where recombination often occurs in the map (the region with high recombination rate) or the region with low frequency recombination (the region where recombination hardly occurs), that is, the color distribution change point in the recombination map.

[0214] For research on recombination hotspots, go back to the gff file of Hg19 to extract related sequences and genes, and get more detailed descriptions of some genes closely related to recombination, thereby verifying the scientificity and feasibility of the scheme of the present invention. from Figure 5 Among them, 103 recombination hotspots can be found, and some related genes (ADAMTS18, PRDM9, ADAM12, etc., a total of 50 genes) have been found according to the gff file of Hg19. It is kn...

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Abstract

The invention relates to a genetic map construction and haplotype analytical method based on single-cell whole genome sequencing, and a device used for the method. The genetic map construction method comprises the following steps: comparing a whole genome sequence of a single cell of a species with a reference sequence to obtain a statistic result of a single nucleotide polymorphic site genotype; performing parent type classification of the genotype result to obtain a most appropriate male parent / female parent (a / b) result, so as to obtain a minimum recombination frequency of all the cells in the statistic result; according to the type classification result, dividing a linkage area (bin); calculating a change ratio of a / b to obtain recombination rates between all adjacent bins; and finally obtaining the genetic map according to the recombination rate of each recombinant site. The method of the invention can obtain a genetic map with high resolution by using a single cell, can not only applicable to human, but also applicable to some higher organisms with limited fertility, especially to endangered species.

Description

technical field [0001] The present invention relates to the fields of genetics and bioinformatics, in particular to a method and device for constructing a genetic map, and a method and device for analyzing a haplotype, in particular to a method and a device for constructing a genetic map based on single-cell whole-genome sequencing, and a haplotype Analytical methods and devices. Background technique [0002] The construction of the genetic map is based on the third law of genetics - the law of linkage and exchange of genes, that is, the genetic markers with genetic polymorphisms are used as "signposts", and the genetic distance (two loci in the event of meiosis The percentage of exchange and recombination between them, 1% recombination rate is called 1cM) is the genome map of the map distance. The construction of genetic maps is of great significance to the study of various species, and can explain the genetic laws and characteristics of species. Using this function, we ca...

Claims

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Application Information

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IPC IPC(8): C12Q1/68C12M1/34C12N15/10G16B25/00G16B30/10
CPCC12Q1/68C12Q1/6874C12Q1/6881C12Q1/6869C12Q2600/172C12M1/34G16B25/00G16B30/00G16B30/10
Inventor 宋卢挺邵迪郑泽群郑智俊吴逵梁舒恒陶晔侯勇
Owner TIANJIN MEDICAL LAB BGI
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