What is Genome wide analysis and Locus specific analysis

Question

[akij]

I am reading some articles on genetic variations and I see there are two types of analysis one is genome wide genetic variation analysis and second one is locus specific genetic variation analysis. I don't understand what these two, genome wide and locus specific analysis mean and what is the difference between these two analysis or why do we need both type of analysis?

Answer 1

[WouterDeCoster]

The terms are pretty self-explanatory. A genome-wide analysis is an analysis performed across the entire genome. A locus-specific analysis is an analysis performed specific in one locus (region) of the genome.

Essentially: genome-wide is unbiased (you look everywhere), locus-specific is hypothesis-driven (this locus should contain interesting variants). Genome-wide is probably more expensive (you sequence more), but that depends on the technology used by either approach.

[theobroma22]

Does genome-wide also refer to comparing across genomes such as for example studies among mice, primate, fungi and human? Is genome-wide an exclusive area of genomics or can it refer to other 'omics' analyses like proteomics?

[WouterDeCoster]

Not sure if there is a proper ontology of this, but my interpretation:

Does genome-wide also refer to comparing across genomes such as for example studies among mice, primate, fungi and human?

That would be meta-genomics, I guess, or comparative genomics. Depends.

Is genome-wide an exclusive area of genomics or can it refer to other 'omics' analyses like proteomics?

Well there are also terms like transcriptome-wide or proteome-wide analysis (such as respectively RNA-seq or mass spec), in contrast of targeted approaches such as qPCR or Western blot.

[akij]

So what I understand is that, Genome wide SNP analysis means detection of SNPs in whole Genome, this gives us the location of the SNP and then this Location specific analysis is done on different people to find out if that SNP is present in certain group of people(Europe/Asian for example)?

[WouterDeCoster]

The answer to that question fundamentally depends on the technology used: SNP-array or sequencing.