select sets

[Chaim Schramm]

1. What is considered the minimum acceptable size of a select set?
2. If there aren't enough unmutated sequences for a select set, should I still include a putative novel allele in the genotype, even if I don't submit it for review on it's own? If not, how should I indicate that I am manually filtering the output of the inference tool?
   
3. If I combined to samples from the same donor to do inference, should I generate a select set for each sample, or is a select set from one of the samples sufficient?

Thanks,
Chaim

[William Lees]

I'm copying Christian and Andrew explicitly, for views on what they think NIH and IARC are looking for here in terms of acceptability.

re. 2 - please upload the entire genotype.  OGRDB asks you to pick the alleles that you wish to submit, so it doesn't matter to the tool if there are others listed that you choose not to submit. You might want to comment in the Notes on the rationale for picking some and not others, but showing the entire genotype is, I think, important to put the inferences in context.

All the best

William

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[Schramm, Chaim (NIH/VRC) [E]]

#3 is answered in the documentation at https://github.com/airr-community/airr-standards/blob/ogre/docs/ogre/iarc_submission_ncbi.rst, which I didn't read carefully enough: generate a select set from each sample.

Per Mats, the answer to #1 is no specific minimum, but it may be helpful to submit other supporting information (eg TIgGER or partis plots) if there are few or no unmutated sequences.

~CH

--
Chaim A. Schramm, PhD
Staff Scientist, Genome Analysis Core
Vaccine Research Center
NIAID, National Institutes of Health
Bethesda, MD 20892

chaim....@nih.gov

301-761-7296

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From: William Lees <wil...@lees.org.uk>
Sent: Thursday, November 1, 2018 1:52:02 PM
To: ogrdb-di...@googlegroups.com; Christian Busse; Andrew Collins
Subject: Re: select sets

 

To view this discussion on the web, visit https://groups.google.com/d/msgid/ogrdb-discussion/3a6d7ca8-0a94-c8ac-1f8a-91fe580a0411%40lees.org.uk.

[Andrew Collins]

Hi Chaim,

I am preparing for Friday's IARC meeting, and I wonder how things are going with your sequence submissions. I don't think I have seen any news since early in November. Are there any remaining issues we can deal with? Would you be interested in trying the submit your sequences via the OGRDB? We are keen to begin new evaluations, as we would like to have a large set of sequences evaluated by the time of the Genoa meeting. Please let me know if there is anything we can do to facilitate the submission.

with best wishes

Andrew

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From: Schramm, Chaim (NIH/VRC) [E] <chaim....@nih.gov>
Sent: Friday, 2 November 2018 5:37:04 AM
To: William Lees; ogrdb-di...@googlegroups.com; Christian Busse; Andrew Collins
Subject: Re: select sets