Welcome to the world of "bioinformatics"
The following is an introduction to the literature.
About the detection and analysis of positive selection signals in the human genome.
Positive selection: A certain mutation site gradually accumulates and becomes an advantageous site.
The specific performance is as follows: as time goes by, the frequency of mutant genotypes at this site becomes higher and higher, far exceeding the wild type;
By comparing domesticated/wild animals and plants, Modern Homo sapiens/primates, specific populations/reference populations, etc. are used to find genomes subject to positive selection.
Explain the relationship between a genome under positive selection and a specific phenotype.
There are many ways to detect positive selection. Let’s take a document as an example to introduce how to tell a story around positive selection.
Literature source "Detecting signatures of positive selection associated with musical aptitude in the human genome"
Research sample: 283 unrelated Finns.
Research phenotype: Divide these 283 samples into two parts according to musical ability. Case is a person with relatively high musical ability, and control is a person with no musical talent.
Genotype: Illumina HumanOmniExpress 12 1.0?V SNP chip
Forward selection analysis method: haploPS, XP-EHH, and Fst are used here to scan forward selection bits point.
Genomic regions with a P value less than 0.05 in the case sample, and in the control sample, these significant genomic regions did not reach a significant level.
The sites with XP-EHH scores reaching the top 0.1% are selected as sites for positive selection.
The sites with Fst values ??in the top 1% are used as sites for positive selection.
Genetrail2 tool (rail2.bioinf.uni-sb.de/) was used for biological function annotation.
The biological function annotation results show that the positively selected sites and genes (DICER1, FGF20, CUX1, SPARC, KIF3A, TGFB3, LGR5, GPR98, PAX8, COL11A1, USH2A, and PROX1) are mainly related to related to the development of the inner ear.
The above is a combination of multiple natural selection tools to illustrate the relationship between genes and phenotypes of positive selection.
Of course, different literatures will have slightly different threshold settings for these natural selection tools.
That’s it for today’s literature interpretation.
The so-called learning from other people's literature and doing your own analysis.
I hope all readers will gain something!