Indels in DNA Sequence Alignment

Question

[dralka.vet]

I wish to know about method to confirm that insertions shown in alignment are real and not artifacts of alignment.

Thanks Alka

[finswimmer]

Do sanger sequencing.

fin swimmer

[dralka.vet]

The sequence obtained by sanger sequencing only and electropherogram files looks clean, sending samples again for sequencing will economically burden the lab. However, before reporting I want to be sure.

Regards

[finswimmer]

So we are talking about Sanger Sequencing data only? Is the insertion homozygous or heterozygous?

[dralka.vet]

The sequence received is by Sanger sequencing and it is RNA virus gene.

[Kevin Blighe]

Sanger is the usual method for confirming variants. If you want another method, think about something like real-time PCR or MLPA, with primers/probes targeting the inserted sequence. As an example, real-time PCR can accurately measure HER2 duplications in HER2-positive breast cancer (I know because I have developed assays for this).