[CIS PIDD] [cis-pidd] A Gene Panel for PID Testing by NGS

[Chang, Elizabeth]

Dear Dewton,

Thank you very much for excellent suggestions and comments, and also for sending samples.  I left out some extremely rear genes on the first panel because of high cost and size limit.  It seems some of them are important and no so rare.  I will include the suggested genes in the next modified panel.  Next year we may be able to do exome sequencing.

Kind regards,

Elizabeth (Yenhui)

From: Dewton Vasconcelos [mailto:dmvascon at usp.br]
Sent: Wednesday, October 23, 2013 9:50 AM
To: CIS-PIDD
Subject: Re: [cis-pidd] A Gene Panel for PID Testing by NGS

Dear Elizabeth, good morning

Thank you for your kindness in offering the sequencing service.
The list of genes is very interesting. Several suggestions are very interesting too.
I think STAT1 is of paramount importance, maybe others associated with CMC (IL17F, IL-17RA, CARD9)
I would like to ask about the possibility of adding some genes associated to B cell defects not accessible to flow cytometry screening, such as AID, UNG and IKBA, maybe CD40.
Looking for T cell defects I think besides those suggested MAGT1 and UNC119 (that are XL and AD) are interesting too.
DOCK 8 is very difficult to sequence by NGS, as most mutations are multiexonic, so for evaluating insertions or deletions MLPA is fundamental.

We also have some samples that we would like to send, with a defined phenotype and unknown genetic defect.

Best regards,

Dewton


Dewton de Moraes Vasconcelos, MD, PhD

Primary Immunodeficiencies Outpatient Unit ADEE3003

Lab. of Medical Investigation Unit 56

University of São Paulo School of Medicine
Chang, Elizabeth wrote:

Dear All,



I have been working on a gene panel to assist the diagnosis of Primary Immunodeficiency diseases using next generation sequencing (NGS) technology.  Please see attached gene list.  I would appreciate to hear your opinion about the panel and what other genes you would like to see included.  I have run 24 samples of known PID patient with good results.  We are seeking more PID samples for validation.  If you have any interesting samples we would be pleased to run them free of charge.  However, we need these by November 22nd, 2013.   You can mail samples to,



Dr. Yenhui Chang

Department of Pathology and Laboratory Medicine

All Children's Hospital

501 Sixth Avenue South

St. Petersburg, Florida 33701

Laboratory: 727-767-4976



The samples can be EDTA blood, DNA, or saliva.  I can provide saliva collecting kit.  Please include a brief description of the disease symptoms and a summary of lab test results.


Your opinion is highly appreciated.



Yenhui Chang


Yenhui Chang, MD, PhD, D.ABHI
Section Director, Histocompatibility and Immunogenetics
Department of Pathology and Laboratory Medicine
All Children's Hospital
Johns Hopkins Medicine
St. Petersburg, Florida 33701
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Office: 727 767 4230
Laboratory: 727 767 4976
Fax: 727 767 8367


CONFIDENTIALITY NOTICE: This E-mail message, including any attachments, is for the sole use of intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply E-mail and destroy all copies of the original message and its attachments without reading or saving in any manner. Thank you xxvii

---

The CIS-PIDD listserv is supported by:

[http://www.clinimmsoc.org/UserFiles/image/cis-pidd-list-logo_v1.jpg]
The science & practice of human immunology

P: +1.414.224.8095
E: info at clinimmsoc.org<mailto:info at clinimmsoc.org>

Not a member of CIS? Please visit www.clinimmsoc.org<https://cis.execinc.com/edibo/Signup> to join!

You are currently subscribed to cis-pidd as: dmvascon at usp.br<mailto:dmvascon at usp.br>.
To unsubscribe click here: http://lm.clinimmsoc.org/u?id=183824445.7c17faf92455fedf52e07cbdec8fae72&n=T&l=cis-pidd&o=43997795


---

The CIS-PIDD listserv is supported by:

[http://www.clinimmsoc.org/UserFiles/image/cis-pidd-list-logo_v1.jpg]
The science & practice of human immunology

P: +1.414.224.8095
E: info at clinimmsoc.org<mailto:info at clinimmsoc.org>

Not a member of CIS? Please visit www.clinimmsoc.org<https://cis.execinc.com/edibo/Signup> to join!

You are currently subscribed to cis-pidd as: Elizabeth.chang at allkids.org<mailto:Elizabeth.chang at allkids.org>.
To unsubscribe click here: http://lm.clinimmsoc.org/u?id=203479868.2c5c9e7c15b42083823d99ce933a1d9a&n=T&l=cis-pidd&o=44005519

CONFIDENTIALITY NOTICE: This E-mail message, including any attachments, is for the sole use of intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply E-mail and destroy all copies of the original message and its attachments without reading or saving in any manner. Thank you xxvii

---
The CIS-PIDD listserv is supported by the Clinical Immunology Society
The science & practice of human immunology

P: +1.414.224.8095
E: info at clinimmsoc.org

Not a member of CIS? Please visit www.clinimmsoc.org to join!

You are currently subscribed to cis-pidd as: pagid at list.clinimmsoc.org.
To unsubscribe click here: http://lm.clinimmsoc.org/u?id=183939985.3ea13d40a15475ac00ebbd9cd8a37d6d&n=T&l=cis-pidd&o=44007258
or send a blank email to leave-44007258-183939985.3ea13d40a15475ac00ebbd9cd8a37d6d at lists.clinimmsoc.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://seven.pairlist.net/pipermail/pagid/attachments/20131023/e485a5cb/attachment-0001.html>