Whole Genome Sequencing IG regions

Question

[719]

I am looking at some sequencing data in https://doi.org/10.1038/s41588-024-01853-0 and am particularly interested in the loci around the immunoglobulin regions, on Chromosomes 2,14 & 22. They use Illumina HiSeq2000 & HiSeq2500 and a large chunk of somatic mutations found are in or around the immunoglobulin genes, and many not in V genes. Worth noting this is from plasma cells, that will have undergone recombination and somatic hypermutation as these loci. Is this data interesting or did more need to be done to ensure correct mapping of reads etc?

Thanks in advance

[Pierre Lindenbaum]

please define "interesting"

[ATpoint]

The question is what you are after. Is this a disease setup, or...well, what is this all about. Generally, these regions are hotspots of hypermutation, so a lot of varians are expected. Is there a scientific question at hand or are you fishing for a project?

[719]

Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main concern is that given there are SHM & recombination in these regions, are the calls I am seeing reliable or should I take them with something of a pinch of salt?

[GenoMax]

are the calls I am seeing reliable or should I take them with something of a pinch of salt?

Not sure what calls you are referring to but the sequence basecalls should be reliable considering this appears to be a recent paper (though HiSeq 2K and 2500 are older sequencers and the data could be several years old before it got published in 2024, we have no way to know).

You will need to decide what kind of error you are willing to allow when you align the reads (this is not always an easy setting with aligners and may not be always available) and if the end result suits your purpose.