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Old 02-03-2016, 02:45 PM   #1
nurmp89
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Default Sanger sequencing chromatograms will look like what for heterozygous mutation?

Hello,

I have a question: For heterozygous deletion, Sanger sequencing chromatograms will look like what?

This is because, I found heterozygous deletion in 1 sample when i did ion torrent sequencing. Brief information about that mutation is below with IGV figure.

Chr Start End Ref Alt Func.refGene Gene.refGene
chr1 155208272 155208276 AGGGC AGGC intronic GBA

PD272 Ion Torrent - IGV.pngPD272 Ion Torrent - IGV 2.PNG

I validate this mutation using Sanger sequencing and I got this result. Does this result correct? Does it is represent heterozygous deletion?

PD272 Sanger - Reverse.PNG
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Old 02-04-2016, 01:48 AM   #2
Bukowski
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Normally a het indel in a Sanger trace will mean you end up with superimposed traces. See:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2429969/

You don't actually show the read support in IGV in your screenshots, but from the pop up it looks pretty minimal. Looks like the reference sequence to me.

Last edited by Bukowski; 02-04-2016 at 01:51 AM.
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Old 02-16-2016, 05:20 AM   #3
sklages
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Quote:
Originally Posted by nurmp89 View Post
Hello,
I validate this mutation using Sanger sequencing and I got this result. Does this result correct? Does it is represent heterozygous deletion?
Attachment 4185
Usually for heterozygous indels the sequence after the start of the mutation is more or less "unreadable" or hard to read due to both alleles being read by the polymerase.

See example here http://www.codoncode.com/aligner/quicktour/indels.htm

best,
Sven
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