Repeating mutations

AGCteam · 12-20-2018, 03:54 AM

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.

torben · 01-04-2019, 04:18 AM

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

AGCteam · 01-04-2019, 05:10 AM

Thank you a lot Torben

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12-20-2018, 03:54 AM	#1
AGCteam Junior Member Location: Bosnia Join Date: Dec 2018 Posts: 2	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.

01-04-2019, 04:18 AM	#2
torben Member Location: Norway Join Date: Oct 2012 Posts: 15	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

01-04-2019, 05:10 AM	#3
AGCteam Junior Member Location: Bosnia Join Date: Dec 2018 Posts: 2	Thank you a lot Torben