Fusion gene detection 2014-Dec 及 TLCN檢體申請

Fusion gene detection 2014-Dec 及 TLCN檢體申請
由 sufang 在三, 01/21/2015 – 11:29 發表 Cholangiocarcinoma cholangiocarcinoma FGFR2 gene fusion

Nov 27, 2014 at 2:57 PM

<910208 mail.kmuh.org.tw=""> To: Su-Fang Lin

Dear SF,

Only minor suggestions (in red color). Are you going to list the oncogenes screening in your proposal or we can just perform the exam?

I am current reading most recent driver mutations in the cholabgiocarcinoma, but I will be great appreciated if you can also give me the most updated/recurrent mutated genes in cholangiocarcinoma. Than I will design primers for those candidate genes.

Furthermore, I do not have a MiSeq in my lab yet, so I outsourcing now. I wish

I can get my own MiSeq machine in one year.

Kindly regards, Daw-yang

Thu, Nov 27, 2014 at 4:34 PM

Su-Fang Lin To: Daw-yang Hwang

Three references for you! Best, Su-Fang

4001_2014_03_New Routes to Targeted Therapy of Intrahepatic Cholangiocarcinomas Revealed by Next-Generatiion Sequencing.pdf

4239_2013_12_Exome sequencing identifies distinct mutational patterns in liver fluke-related and non-infection- related bile duct cancers.pdf

3970_2013_12_Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas.pdf

Daw-yang Hwang <910208 mail.kmuh.org.tw=""> To: Su-Fang Lin

Please see the attached file for the updated TLCN form. Daw-yang

about your application

6 messages

To: “sflin1@gmail.com”

Dear Dr.Lin,

Mon, Dec 1, 2014 at 7:22 PM

Welcome to apply for TLCN samples. However, I need to tell you that many of the cholangiocarcinoma samples are not so good in the RNA quality (due to tumor necrosis), and many have low tumor %. Thus, though we have more than 150 cases, but it is impossible to get 96 cholangiocarcinoma with high tumor % and good RNA quality for your application. we probalbly can give you around 40-50 cases. If you just need DNA and tissue section, it may be possible.

shiufeng

Su-Fang Lin

To: <910208 mail.kmuh.org.tw="">

Dear Daw-Yang,

Mon, Dec 1, 2014 at 9:05 PM

What do you think? Can I tell her that for our purpose not so ok RNA are still worth a try? Thank you very much! SF

Sent from Gmail Mobile

Daw-yang Hwang <910208 mail.kmuh.org.tw=""> To: Su-Fang Lin

Dear SF,

Tue, Dec 2, 2014 at 5:06 AM

I can understand the RNA quality issue. We can try 48 RNA samples first to see how it goes. For DNA, it can be as much as possible, so maybe we should apply 144 DNA samples?

Daw-yang

Su-Fang Lin Tue, Dec 2, 2014 at 9:37 AM To: ,

Dear Dr. Huang,

Thank you very much for telling us the tumor necrosis/poor RNA quality issue. With this regard, we would like to apply 48 RNA samples and associated unstained paraffin sections; and 144 DNA samples of cholangiocarcinoma tissues. A new application form with revised case numbers is attached in the mail.

Thank you very much for your great help!!

Best, Su-Fang

TLCN sample_request_NICR_LinSF v2.pdf 282K

To: Su-Fang Lin ,

144 is too many. Please reduce to 80 to 90 cases.

Do you accept cases with a tumor percentage around 50 percent only? iPhone

Su-Fang Lin To:

Tue, Dec 2, 2014 at 12:25 PM

114太多啊! 真對不起，因為機器一次跑48個所以想說取它的倍數來申請…

好，那我們就申請九十例DNA檢體。另外，50% tumor cellularity 應該是OK的。謝謝妳!

素芳

Re: about your application

9 messages

Sat, Dec 6, 2014 at 9:10 PM

To: Su-Fang Lin Cc:

Please remember to submit a revised form of LOI.

Su-Fang Lin Sat, Dec 6, 2014 at 10:19 PM
To: ,
Dear Dr. Huang,
Enclosed please find my revised LOI.

Again, many thanks for all your advice and help!

Best, Su-Fang

Letter of Intent of TLCN_NICR_SuFangLin v3.pdf

 To: Su-Fang Lin Sun, Dec 7, 2014 at 8:17 AM

You did not change the case number for DNA. Many ICC tumors have low DNA tumor %, and need to use laser capture microdissection, which will be quite expenstive (1000/ 1ug). Anyway, the total number still can not reach 144 cases. Could you reduced to 96 cases (48 wells x2) for DNA?

shiufeng

Su-Fang Lin To: Sun, Dec 7, 2014 at 10:00 AM

咦，我在昨天LOI (v3)有改成90例DNA檢體及50% tumor cellularity. 是還有地方漏掉、沒改到的嗎、還是檔案沒有附檔成功? 讓我再送一次! 麻煩您再檢查一下，不好意思。

Best,

Su-Fang

sfhuang@nhri.org.tw To: Su-Fang Lin Sun, Dec 7, 2014 at 8:42 PM

You only made change in the Item V, but you did not change in Item III, No.2, which is the most important part. I can not revised the LOI for you, since it is in pdf file.

shiufeng

Su-Fang Lin Sun, Dec 7, 2014 at 9:03 PM To:

真是糊塗，不好意思. Best, Su-Fang

sfhuang@nhri.org.tw Sun, Dec 7, 2014 at 9:11 PM

To: Su-Fang Lin

OK. It will be sent out for review.

Shiufeng

Su-Fang Lin To:

Great, thank you very much, Dr. Huang!

sfhuang@nhri.org.tw To: Su-Fang Lin Sun, Dec 7, 2014 at 9:19 PM

you are welcome.

Shiufeng