hg38 Ig regions

Question

[emmanouil.a]

Hi,

I'm looking for the Immunoglobulin regions coordinates in hg38 assembly. I want to exclude them from my CNV analysis.

I know the hg19 regions but I do not want just to liftover them.

Many thanks

[Bastien Hervé]

IgH region or more ?

https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=3492

[emmanouil.a]

Many thanks for you answer, in this way I found that I need!

Best!

[ATpoint]

Please use ADD COMMENT and leave the answer field for answers. Thank you.

[rohitsatyam102]

Hi emmanouil.a. Can you help me how to do that for hg19?

[Viktor Messi]

Hi, do you manage to find hg19 immunoglobulin region? I really appreciate if you could help me

Answer 1

[Erin Haskell | ELIXIR]

You can use Ensembl's BioMart tool.

1. Choose Ensembl Genes
2. Choose Human genes (GRCh38p.12)
3. Click on Filters, expand GENE, scroll down to find biotype and choose all the IG genes. If you're only interested in the primary assembly (excluding haplotypic regions and patches) also expand the REGION section and select all chromosomes, scroll down to find X & Y.
4. Click on Attributes, expand the GENE, choose 'Transcript type', 'Chromosome/scaffold name', 'Gene start(bp)' and 'Gene end (bp)'
5. Click Results button at top of the page, export results to Excel (XLS) and sort results by the Chromosome position to group all together (they are unordered otherwise).

Answer 2

[ATpoint]

Download the annotation files for hg38 (GFF/GTF), e.g. from GENCODE, and then extract genes annotated as Ig/Immunglobulin, followed by coordinate extraction.

Answer 3

[Charles Warden]

I think there are certain things where you would want to use a specialized reference, rather than the typical genome reference.

For example, I think I good starting point to learn more about antibody bioinformatics analysis is IgBLAST (and the command-line version has a link to the IMGT reference sequences)