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This article mainly introduces the relevant knowledge of the method of GWAS Ha-Wen balance test, the content is detailed and easy to understand, the operation is simple and fast, and has a certain reference value. I believe you will gain something after reading this article on the method of GWAS Ha-Wen balance test. Let's take a look at it.

"what is Havin balance? "

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Hardy-Weinberg rule Hardy-Weinberg rule is the most important principle in population heredity, which explains how reproduction affects the gene and genotype frequency of a population. The law was named after the surnames of two scholars, Hardy,G.H (British mathematician) and Weinberg,W. (German doctor), who each discovered it in the same year (1908). They propose that in an infinite random mating population without mutation, migration and selection, the gene frequency and genotype frequency will remain the same from generation to generation. -Baidu encyclopedia

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"how to do the Ha-Wen balance test? "

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"Chi-square fitness test! Whether a population conforms to this situation, that is, to achieve genetic equilibrium, that is, the proportion distribution of the three genotypes of a pair of alleles accords with the formula: p2 allele 2 pqlocyq2 allele Q2 allele Q2 allel The frequency of genotype MM is p2MaginNN, the frequency of Q2MaginMN is 2pq. MN:MN:NN=P2:2pq:q2 . MN this pair of genes in the population to reach this state, that is, to achieve genetic balance. If it does not reach this state, it is a population with genetic imbalance. However, with the random mating in the population, the distribution proportion of this gene frequency and genotype will be maintained, and it will be easier to reach the state of genetic equilibrium. Using the Hardy-Weinberg genetic equilibrium coincidence test method, the calculated gene frequency was substituted, the genotype balance frequency was calculated, and then multiplied by the total number of people, the expected value (e) was obtained. The observed number (O) was compared with the expected value (e), and χ 2 test was carried out. There was no significant difference in genotype distribution between the case group and the control group (P > 0.05), which conformed to the law of genetic equilibrium.

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"what is the difference between Ha-Wen balanced filtration and MAF filtration? "

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Before, I was a little confused about these two concepts, but then I understood it. One of these two concepts is the screening of gene frequency, and the other is the screening of genotype frequency. For a locus "AA AT TT", the frequency of An is the gene frequency and AA is the genotype frequency. MAF is to screen the gene frequency directly, while the Harwin balance test is to infer the ideal (AA,AT,TT) distribution according to the genotype, and then carry on the fitness test with the actual observation, and then get the P value, and screen according to the P value. That is to say, the smaller the P value is, the less the locus is in accordance with the Harbin-Wen equilibrium.

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"two purposes:"

The result of Harbin test for all sites was calculated to delete the loci 1. 5 that did not conform to the Harwin equilibrium in SNP. Calculate the P value plink-- bfile HapMap_3_r3_8-- hardy of the HWE of all sites

Data format of plink.hwe:

IDTEST type A1 minor locus A2 major genotype distribution of CHR chromosome SNP SNP: A1A1, A1A2, A2A2O (HET) observation of heterozygosity frequency E (HET) expected heterozygosity frequency P Chi-square test P-value value of Harwin equilibrium

Result Preview:

two。 Extraction of sites with a Harwin p value less than 0.0001

Here we use awk:

Awk'{if ($9)

Plinkzoomhwe.hwe

There are 123 loci, of which UNAFF is 45 loci.

3. Set the filtering standard 1e-4plink-bfile HapMap_3_r3_8-hwe 1e-4-make-bed-out HapMap_3_r3_9

Log:

Options in effect:

-- bfile HapMap_3_r3_8

-- hwe 1e-4

-- make-bed

-- out HapMap_3_r3_9

515185 MB RAM detected; reserving 257592 MB for main workspace.

1073788 variants loaded from .bim file.

163people (79 males, 84 females) loaded from .fam.

112 phenotype values loaded from .fam.

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 112 founders and 51 nonfounders present.

Calculating allele frequencies... Done.

Total genotyping rate is 0.998136.

Hwe: 45 variants removed due to Hardy-Weinberg exact test.

1073743 variants and 163 people pass filters and QC.

Among remaining phenotypes, 56 are cases and 56 are controls. (51 phenotypes

Are missing.)

-make-bed to HapMap_3_r3_9.bed + HapMap_3_r3_9.bim + HapMap_3_r3_9.fam...

Done.

As you can see, a total of 45 SNP are filtered out according to the P value of Havin, as calculated manually above.

4. Visualization

R code:

Hwe

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