Question

1.

1. In genetics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait.

A) Define the following acronyms:

GWAS, HRM, MAF, Tag SNP

B) Describe how you could use HRM analysis to identify a SNP

C) Explain how to you would design a GWAS study

Answer 1

#1 A

GWAS : "genome wide association study" is the analysis of genome for genetic variants of diffrent individuals to check the association between diffrent genetic regions (focusing sinlge nucleotide polymorphisms) and desease carriying traits.

HRM : "High resolution melt" works under the principle of PCR melting "dissociation curve techniques". It is the powerful analysing technique involving mutation scanning, SNP genotyping and sequence scanning of double stranded DNA samples. It is imployed to detect minor sequence diffrences in (PCR) amplified DNA by melting procedure.

MAF :"minor alle frequeency" or the second most frequent allele occuring in the population. It is empolyed to diffrentiate among common and rare variants of a given population.

Tag SNP : It is a "representative SNP" present in the genome regions representing a group of SNPs-(single nucleotide polymorphism) having high linkage disequilibrium.

B) process of HRM analysis to detect SNP:

• The sample is first amplified by PCR. Intercalting dyes are added during the process. These saturation dyes fluoresce when the double stranded DNA (dsDNA)is present.
• Amplicon is the term used for the amplified region of interest in PCR. Increase in the amplcon concntration also increases the flourescence of dsDNA product.
• the product amplicon is heated gradually starting from 50 degrees to 95 dgrees temprature. At a particular temprature, the melting point is reached when the sample got denatured and melts apart. This melting results in sigle stranded of DNA and the fluoresce fades away because there is no more dsDNA left.
• A graph is plotted against the fluoresce level versus temprature observed in the experiment. It will generate a melting curve. This curve can change when there is a change in even a single base in the given sample.
• High reolution melt curves generally plotted floresce on y- axis and temprature on X-axis.
• 
  Y-axis 95°C X-axis 55°C Temperature
  

in this way SNPs can be identified in a given DNA sample.

C) To design GWAS study two main things have to be considered- first - which locus to genotype is taken secondly the number of individuals to be analysed. GWAs sudy involve comarison of diffrent individual's DNA having varying phenotype of the concerned trait. THese can be deseased individuals or healthy. This is called case control setup. All individuals in the groups are genotyped for common SNPs. For each SNP, check if the allele freuency is altered among the case and ccontrol group. Odds ratio is used to quantify the strength of the association between two groups. In context of GWAs is the ratio of odds of desease for indivisuals of specific allele and odds of desease of individuals lacking that allel. If Allele frequency in the case group (much higher) and the control group is lower observed odd ratio is 1. The objective of GWAs is to find the oddds value diffrent from 1 showing that a SNP is linked with the particular desease.