exome and genome data

Question

[Eliza]

Hi, I downloaded exome data from gnomad to get the allele frequency of some SNPs that I'm analyzing. I noticed that some SNPs ( in my data) are not present in the exome data ( in gnomad) and part of my report question for homework is: "are the ones that are not found outside genes?", what does it mean outside genes? does it mean that they are not in the exome data but in the genome data on gnomad?

i found this in an article:"Single-nucleotide polymorphisms (SNPs) are single base-pair substitutions that occur within and outside genes"

also found this :"SNP markers might be selected outside of exomes or the direct cause of a genetic mutation" does this means that it is found in the genome but not exom data in gnomad? so what outside gemes means?

thank you:)

[Ram]

You've posted your questions on biostars and bioinformatics SE multiple times. This is bad etiquette. At a minimum, wait a few days before seeking help from another community if the one you posted on does not respond. And when you do open a post in another community, point to the existing post on the other community and say you did not receive any response.

Your approach is called shotgun posting - creating posts on multiple forums at the same time so you increase your chances of getting a quick response - this runs the risk of annoying users in both communities and results in problems where you're going to need to update conversations and resolutions on both sites based on progress/changes made to either.

[Ram]

Cross-posted on bioinfo SE: https://bioinformatics.stackexchange.com/questions/20184/snps-location-out-side-the-gene

[Matthias Zepper]

The gnomAD reference can be found here: Exome calling regions and genome calling regions.

[Eliza]

@Matthias zepper what I meant is that I would like to understand what the term "outside gene" means, I read some information online and I understood that gene is the protein part of the genome, so outside of gene is the not protein part? I'm new to genetics and I looked at the references you sent and sadly I can't understand them

[Matthias Zepper]

In that case, I can recommend the respective chapters in any molecular biology book.

Albert's "Molecular Biology of the Cell" is the book on this subject, but personally I like Karp's "Cell Biology" more. In any way, your university's library should have multiple options to choose from, and old issues are even available freely on the NCBI bookshelf: See the DNA to RNA and RNA to protein chapters of Alberts 4th edition for an answer to your question.

For a really high-level overview, learngenomics.dev is geared towards engineers who just need a very coarse understanding of biology.

[Eliza]

Thank you :) It would really help just for the sake of this homework to understand what is SNP outside gene : does it mean that the snp is not in the exome but outside the protein coding the other part of the genome?

[Matthias Zepper]

My point is: The answer will likely not help you without having understood the fundamentals.

But here you go:

• The genome is the entirety of the genetic information found in a cell.
• Genes make up a fraction of the genome (greatly varies depending on the organism).
• The part of the genome, that doesn't lie within genes, is called intergenic.
• Many genes, but not all, are protein-coding.
• Each gene can be divided into several, partly overlapping, functional parts. Introns and exons are two of them. Most genes have multiple exons with introns between them.
• The exome is the entirety of the exonic parts of genes, most exonic parts are protein-coding.
• An exome panel is the part of the exome that can be investigated for technical reasons.
• gnomAD uses a specific exome respectively genome panel. Due to technical reasons, the panels comprise only a subset of the exome and genome.

Hence, a SNP that falls outside the gnomAD exome panel:

• May nonetheless be part of the exome, if it can't be assayed for technical reasons. Most likely, it is not part of the exome.
• If it is not part of the exome, it is also not-protein coding. But it may still be within a gene (e.g. in an intron or one of the other functional parts).
• If it is outside a gene, it may still influence the function of a gene.

PS: Also be careful to stick to "protein-coding part of the genome". When you speak of the "protein part of the genome", a cell biologist may think of nucleosomes, cohesin, CTCF, transcription factors and such.