Shulou(Shulou.com)06/01 Report--

Today, I would like to talk to you about what GWAS analysis based on family data is like. Many people may not know much about it. In order to make you understand better, the editor has summarized the following contents for you. I hope you can get something from this article.

Through GWAS analysis, we can find the mutation sites related to a disease or trait. The traditional GWAS is based on the design of control/case. By comparing the differences of mutation sites or genotype frequencies between healthy people and sick people, the relevant sites are finally determined.

For family inherited diseases, the above analysis strategy is problematic. In the family, there is a genetic relationship between individuals of different generations, and disease-related loci will also be passed on from father to offspring. In order to take this transmission relationship into account, a new analysis method, TDT, is proposed for the GWAS analysis of family hereditary diseases.

The full name of TDT is TRANSMISSION DISEQUILIBRIUM TEST. By analyzing the difference between the number of allel inherited from the parent and the expected number of allel, we can judge whether the change point is related to the disease.

In the above diagram, the offspring inherit M1allel from the homozygous parent and M2 allel from the heterozygous parent. The allel passed from the parent to the offspring is called transmitted allel.

For a SNP locus, count the number of transmitted allel and non-transmitted allel in the sample and get the following table

The statistics of the TDT test are calculated as follows

(B-c) ^ 2 / (b + c)

This statistic accords with the chi-square distribution with 1 degree of freedom.

Plink software can be used for GWAS analysis of family data, and the usage is as follows

Plink-file mydata-tdt

A plink.tdt file is generated, where each column has the following meaning

ColumnMeaningCHRChromosome numberSNPSNP identifierA1Minor allele codeA2Major allele codeTTransmitted minor allele countUUntransmitted allele countORTDT odds ratioCHISQTDT chi-square statisticPTDT asymptotic p-valueA:U_PARParental discordance countsCHISQ_PARParental discordance statisticP_PARParental discordance asymptotic p-valueCHISQ_COMCombined test statisticP_COMCombined test asymptotic p-value

The mutation site with P value less than 0.05 is considered to be related to the disease. In addition to TDT testing, plink also supports other more verification methods.

After reading the above, do you have any further understanding of GWAS analysis based on family data? If you want to know more knowledge or related content, please follow the industry information channel, thank you for your support.

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