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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
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Is there Homsap IGHV5-10-1 in MiXCR? #327

Closed MathildeFogPerez closed 6 years ago

MathildeFogPerez commented 6 years ago

Dears,

I used the latest version of MiXCR (2.1.8) and one of my antibody sequence was assigned to IGHV5-51*00(1161). But it should be assigned IGHV5-10-1 (confirmed by IMGT). The sequence is: GAAGTGCAGCTGGTGCAGTCCGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAGGATCTCCTGTGAGGCTTCTGGATACAGCTTTATCAGTTTCTGGATCAACTGGGTGCGCCAGATGCCCGGGAAAGGCTTGGAGTGGATGGGGAGGATTGATCCTAGTGACTCTTATACCGACTACAGCCCGTCCTTCCAAGGCCACGTCACCATCTCAGCTGACAAGTCCATCAGCACTGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGATCCCCTCACGGGGGGTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG

Then I checked a repertoire that I run previously with MiXCR version 2.1.5, and none of the 100.000 sequences was assigned to IGHV5-10-1. So I am wondering if you removed this vGene in MiXCR? That would be a problem for my analysis, since I use the info related to the Valignment, it gives me too many mutations with IGHV5-51.

Thanks a lot in advance. Best, Mathilde

dbolotin commented 6 years ago

Dear Mathilde,

Thanks for reporting this!

You can directly use IMGT library in MiXCR, please see corresponding section: http://mixcr.readthedocs.io/en/latest/importSegments.html#imgt-library Here is the link to the most recent library: https://github.com/repseqio/library-imgt/releases/download/v2/imgt.201802-5.sv2.json.gz

Our default reference is based on genomic assemblies, namely IGH is currently based on NG_001019.5, and there is no IGHV5-10-1 in that contig. NCBI updated the sequence with NG_001019.6, where, as I understand, IGHV5-10-1 is present, however, unfortunately, we missed this event to update our internal library.

We will update the repseqio library to reflect updated information, ASAP. However it will take several weeks to check everything.

I will leave this issue opened until then.

Best, Dmitry.

MathildeFogPerez commented 6 years ago

Thank you for your answer, Dmitry! I will wait for your library to be updated then, I prefer. Best, Mathilde

dbolotin commented 6 years ago

Fixed in 5712b1dfe828371fdc7518673a1758a7b0c30b7e with the new library.