Question

8. A recent genome-wide association study was done to find loci associated with schizophrenia and the data is shown in the figure. Use this figure to answer the following questions. PGC2 + Chinese 30 Nature Genetics volume 49 pages 1576-1583 (2017) (d)601- -10 Chinese only 1 2 3 4 5 6 16 18 20 22 7 8 9 10 11 12 13 14 Chromosome 1) What is the name for this type of chart? Why did they only use a Chinese population for this study? Which chromosome contains the most significant association and in which region (por 9)? iv Why didn't they use other more targeted molecular methods to find genes that cause schizophrenia?

Answer 1

i) The name of the plot is Manhattan plot that is a type of scatter plot and is mostly used to display data with a large number of data-points. It is commonly used in genome wide association studies to find Single Nucleotide Polymorphism.

ii) They only used Chinese data because the plotting shows data from PGC2 (Psychiatric Genomics Consortium) GWAS data sets. There is no specific reason to choose this data other than this.

iii) The chromosome number 6 contains the most significant association as GWAS is related to SNP differences which lead to phenotypic differences. And the region is p which is apparent from the figure.

iv) The study that is mentioned in the figure has data sets of Chinese schizophrenia cases which are performed further transancestry meta-analyses. Effective treatments are needed for schizophrenia. For this targeted molecular methods will consume more time and also it is not humanly possible to first experiment molecular methods on particular locus and keep the data generated and compare with the present or recent data. This is where GWAS comes into picture. GWAS provides unbaised assessment of SNP across the entire genome. Alongwith that it has the capacity to implicate the specific variants that may be linked to the disease. We can also target large number of sample size. Apart from this it provides various relevant insights into the biological processes that give rise to the disease. Though Next generation sequencing will one day become the primary genotyping method to understand and detect various diseases.