presence of TRBJ gene (TRBJ1-4, TRBJ1-3, and TRBJ1-1) in BCR bulk repertoire seq of Heavy and Light chain

[singhd6]

I analyzed my Bulk BCR rep in MIXCR and in one of my samples's sequencing results I see the TRBJ genes expression as output of J usage. Could it be pseudogene expression and negligible.
mixcr analyze neb-mouse-rna-xcr-umi-nebnext
JA_10_S1_R1_001.fastq.gz
JA_10_S1_R2_001.fastq.gz
result1/JA_10_S1_1
This is the result of post analysis individual.

Just curious.
Thank you
Divya

[mizraelson]

It can also be a small contamination. I would just filter off these clones, if the fractions are low I don't think there is anything to worry about.

[singhd6]

Dear Mark, Good morning. Thank you so much for your prompt response. Yes, the TRBJ clones are 3 in numbers and negligible out of total clones count which is 39604. Thank you Divya

…

________________________________ From: mizraelson ***@***.***> Sent: Thursday, May 8, 2025 7:33 AM To: milaboratory/mixcr ***@***.***> Cc: Singh, Divya Jyoti ***@***.***>; Author ***@***.***> Subject: [EXT] Re: [milaboratory/mixcr] presence of TRBJ gene (TRBJ1-4, TRBJ1-3, and TRBJ1-1) in BCR bulk repertoire seq of Heavy and Light chain (Discussion #1943) PROCEED WITH CAUTION: Slow down and pay close attention to emails sent from outside the organization. If you receive an unsolicited email from an unknown sender or are suspicious of the tone, style, vocabulary or urgency of the email message, never click links or open attachments within it. When in doubt, you should either delete the email, verify its authenticity by contacting the sender using an alternative method not listed in the email, or submit it via the BlueFish button in Outlook for investigation. If you don't have the BlueFish button or are using a mobile device, forward the email as an attachment to ***@***.******@***.***?subject=Report%20a%20Suspicious%20Email>

________________________________ It can also be a small contamination. I would just filter off these clones, if the fractions are low I don't think there is anything to worry about. — Reply to this email directly, view it on GitHub<#1943 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BH7E6ZIMC2EFE2UWBGY3ARL25M6HPAVCNFSM6AAAAAB4URBDNCVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTGMBXGQZTAMQ>. You are receiving this because you authored the thread. Please consider the environment before printing this e-mail Cleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.