What are the types of variants Next Generation Sequencing technologies can find?

Question

[davehresearch]

By using NGS technology, genetic variants between the patient's DNA sequence and the reference genome can be found. Are these variants same as mutations or do they have two different meanings?

In HGVS nomenclature, DNA sequences are represented by c., genomic sequence variants by g., protein changes by p. and mitochondria by m.. Do all these changes fall into the variants category? And what are the differences in them? In ClinVar I have only seen c. variants. Does that mean ClinVar only has information on DNA sequence variants?

To what category SNPs, insertions, deletions, indels fall?

Answer 1

[Devon Ryan]

You might want to take a few genetics classes before dealing too much with these sorts of databases.

All mutations are variants, but not all variants are mutations. In short, a mutation is generally a variant with a deleterious effect (i.e., you have to make some sort of value judgement about its effect).

Variants are represented in transcript/cDNA coordinates by the c. nomenclature. c., g., etc. are just coordinate systems, since obviously a genomic variant in a coding sequence will have a c. and g. coordinate (and often a p. too, of course). Nucleotide-level coordinates can always be mapped to protein-level coordinates (assuming a variant is in a coding region), so typically those are stored. Further, one can always convert between transcript (cDNA) and genomic coordinates, but it's often convenient to just leave things at the transcript level since that's what people have historically wanted.

To what category SNPs, insertions, deletions, indels fall?

All of them can be represented in any of the appropriate coordinate systems.

[davehresearch]

Hey! Can you please give me an answer for this question?

What information about VARIANTS are found in biomedical literature rather than diseases?