Ion Torrent Sequencing

[qnc]

Any one had any experience or knowledge of this technology

here is the pdf
http://is.gd/XmCxQJ

here is their YouTube videos
http://www.youtube.com/iontorrent

It seems like they have sample sizes of 100bp I wonder if they have any way of sequencing across SINEs, LINEs and other areas excluded by Repeat Masker.

Also does it have a quencher/wash step between incorporations so that lengths of homogenous nucleotides can be distinguished i.e. the difference between 6 or 8 of the same nucleotide in a row.

Any help is good.

Thaks

[genlyai]

There are supposedly some in the wild now, so hopefully we should be hearing reports soon.

As for this question:

Originally Posted by qnc

Also does it have a quencher/wash step between incorporations so that lengths of homogenous nucleotides can be distinguished i.e. the difference between 6 or 8 of the same nucleotide in a row.

No, the nucleotides are just normal dNTPs, so the only way to distinguish between 6nt and 8nt homopolymer runs is by the size of the peak on the pH meter.

[GW_OK]

You guys can also go read what everyone else is saying in The Pipeline subforum.

[qnc]

Originally Posted by GW_OK

You guys can also go read what everyone else is saying in The Pipeline subforum.

Thanks still working my round the site so much info its great here.

Originally Posted by genlyai

No, the nucleotides are just normal dNTPs, so the only way to distinguish between 6nt and 8nt homopolymer runs is by the size of the peak on the pH meter.

Will read up about it in the pipeline forum but wanted to know if there was a limit to the number of these that can be in a row to be read. e.g. 454 I think can only read 6-8 in a row is that correct. So the peak hight of 10 in a row is no more than 8. apparently.

But Happy to learn if someone knows different.

Thanks all.

[ak483516]

I have included this basic math question in past student molecular diagnostic exams but find a high fail rate. Any suggestions?

Q. An Ion Torrent Proton 2 chip contains 660 million wells, of which 50% typically yield useable sequencing data, with an average read length of 100bp. How many Proton 2 chips would be needed to sequence the entire human genome with a 20X coverage?

[NextGenSeq]

The P2 chip isn't released yet and the read length of the P1 is currently 200 bp. The P2 chip will supposedly generate 60GB which is 20X coverage.

The haploid human genome is 3 GB
so using your erroneous assumptions above

100 x (3GB/330 million) gives ~900X coverage.

Are you sure this isn't for your own homework?

[hknyrt]

Hi;

What is Brca1 name for Ion Torrent?
or
FANCD2= BRCA2