class12

Section 1: Proportion of G/G in a population

Downloaded a CSV file from Ensemble < https://useast.ensembl.org/Homo_sapiens/Variation/Sample?db=core;r=17:39894595-39895595;v=rs8067378;vdb=variation;vf=959672880#373531_tablePanel

Here we read this CSV file

mxl <- read.csv("373531-SampleGenotypes-Homo_sapiens_Variation_Sample_rs8067378.csv")
head(mxl)

  Sample..Male.Female.Unknown. Genotype..forward.strand. Population.s. Father
1                  NA19648 (F)                       A|A ALL, AMR, MXL      -
2                  NA19649 (M)                       G|G ALL, AMR, MXL      -
3                  NA19651 (F)                       A|A ALL, AMR, MXL      -
4                  NA19652 (M)                       G|G ALL, AMR, MXL      -
5                  NA19654 (F)                       G|G ALL, AMR, MXL      -
6                  NA19655 (M)                       A|G ALL, AMR, MXL      -
  Mother
1      -
2      -
3      -
4      -
5      -
6      -

table(mxl$Genotype..forward.strand.)

A|A A|G G|A G|G 
 22  21  12   9 

(table(mxl$Genotype..forward.strand.)/nrow(mxl)) * 100

    A|A     A|G     G|A     G|G 
34.3750 32.8125 18.7500 14.0625 

Now let’s look at a different population. I chose what the professor chose, which is GBR.

gbr <- read.csv("373522-SampleGenotypes-Homo_sapiens_Variation_Sample_rs8067378.csv")
head(gbr)

  Sample..Male.Female.Unknown. Genotype..forward.strand. Population.s. Father
1                  HG00096 (M)                       A|A ALL, EUR, GBR      -
2                  HG00097 (F)                       G|A ALL, EUR, GBR      -
3                  HG00099 (F)                       G|G ALL, EUR, GBR      -
4                  HG00100 (F)                       A|A ALL, EUR, GBR      -
5                  HG00101 (M)                       A|A ALL, EUR, GBR      -
6                  HG00102 (F)                       A|A ALL, EUR, GBR      -
  Mother
1      -
2      -
3      -
4      -
5      -
6      -

Find portion of GIG

round(table(gbr$Genotype..forward.strand.)/nrow(gbr)*100,2)

  A|A   A|G   G|A   G|G 
25.27 18.68 26.37 29.67 

This variant that is associated with childhood asthma is more frequent in the GBR population than the MKL population.

Let’s now dig into this further.

Section 4: Population Scale Analysis

One sample is obviously not enough to know what is happening in a population. You are interested in assessing genetic differences on a population scale. So, you processed about ~230 samples and did the normalization on a genome level. Now, you want to find whether there is any association of the 4 asthma-associated SNPs (rs8067378…) on ORMDL3 expression.