SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
repeating chipseq or chipseq with another antibody hawainpanda Sample Prep / Library Generation 2 03-12-2015 04:56 PM
How to count the repeating times of a certain 11bp long sequence HSV-1 Bioinformatics 3 02-06-2013 12:04 AM
How to differentiate driver mutations from common/random mutations and SNPs in cancer kumardeep RNA Sequencing 0 09-04-2012 02:51 AM
trouble repeating a BWA alignment command efoss Bioinformatics 0 08-09-2011 02:51 PM
Repeating a SOLiD Focal Map pmiguel SOLiD 2 09-09-2010 04:34 AM

Reply
 
Thread Tools
Old 12-20-2018, 03:54 AM   #1
AGCteam
Junior Member
 
Location: Bosnia

Join Date: Dec 2018
Posts: 2
Default Repeating mutations

Good evening people,

I am working in a lab where we use S5 IonTorrent sequencer and we are sequencing with Colon and Lung V2 panel different type of samples: colon cancers, lung cancers, ovarian cancer, liver cancer, also we sequenced few samples from buccal swab for experiment. In 80% plus samples sequenced with this NGS panel we detect 4 repeating mutations: FGFR3:1807894 G>A; TP53:7579472 G>C; EGFR:55228053 A>T; EGFR:55249063 G>A. At first we thought it was contamination then we repeat same samples with re isolated DNA and we got same result, also we changed library preparation kit, we also asked for colleagues who used same panel do they get same mutations and they do. After 2 years of sequencing we conclude it is not contamination but something different. Could you, please, give me some information about this issue we have?

Sincerely AGC team.
AGCteam is offline   Reply With Quote
Old 01-04-2019, 04:18 AM   #2
torben
Member
 
Location: Norway

Join Date: Oct 2012
Posts: 15
Default

All of these are common variants, see below for allele frequencies from The 1000 Genomes Project. Your frequencies will vary depending on the genetic background of the samples.
FGFR3:1807894 (rs7688609) G=0.0439 A=0.9561
TP53:7579472 (rs1042522) G=0.4571 C=0.5429
EGFR:55228053 (rs1558544) A=0.2266 T=0.7734
EGFR:55249063 (rs1050171) G=0.5673 A=0.4327
torben is offline   Reply With Quote
Old 01-04-2019, 05:10 AM   #3
AGCteam
Junior Member
 
Location: Bosnia

Join Date: Dec 2018
Posts: 2
Default

Thank you a lot Torben
AGCteam is offline   Reply With Quote
Reply

Tags
egfr, repeating mutations, strange mutations, tp53

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:00 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO