Question

SNPs on a single transcript of a gene with multiple transcripts

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3.7 years ago

hkarakurt ▴ 180

Hello, I am doing WGS analysis and I have a question. As you know some genes have multiple transcripts in the genome. E.g. BRCA1 has about 30 transcripts. As I understand one of the transcripts is enough to produce the related protein and transcription of the transcript is highly associated with tissue/cell type. Is there a way to determine or score the transcript importance? If I have a SNP on one of the transcripts, how should I treat this information? WGS data comes from blood samples so I cannot consider the experimental data source.

Thank you in advance.

WGS WES SNP Gene • 1.0k views

ADD COMMENT • link updated 3.7 years ago by caggtaagtat ★ 1.9k • written 3.7 years ago by hkarakurt ▴ 180

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If I have a SNP on one of the transcripts, how should I treat this information?

How was this judgement made? Are there tens of reads supporting that SNP? How is the transcript containing the SNP different than others for this gene (e.g. intron retention, extra exon)?

ADD REPLY • link 3.7 years ago by GenoMax 141k

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It was a hypothetical question. I meant if only one transcript of a gene have a SNP, how should I treat it? Is there any "main transcript annotation" of a gene or a scoring system.

ADD REPLY • link 3.7 years ago by hkarakurt ▴ 180

score 3 · Accepted Answer · 2020-08-11

There are a few project, which tried to indentify the "main transcript" of genes, like the MAIN or APRIS project. If you are working with ensembl, the entries are marked in the transcript table of a gene. However, its not like one cell type only has one transcript isoform and the other cell type only the other. You can have multiple transcript in the same cell. As you know, a SNP, detected in a transcript, most of the times does originate from a variation of the respective DNA sequence. Therefore, a SNP theoretically has the potential to influence the abundance of every possible transcript of that gene, for example when disturbing transcription start sites or the start codon. But as a start, you could check if there is a "main" transcript declared and if there are amino acid changes as a result from the SNP. Then you could check if the SNP may influence splicing, for example with the VarCon R-package.