Learn Sequencing Practically

Question

[Vikas Bansal]

Hi,

I am doing data analysis (dna, rna etc) for my PhD but I am also interested in learning how to generate data. I know how sequencing machines (illumina, 454 etc) works but I learnt that only from papers and internet. I asked 2 groups in my institute (who does sequencing on daily basis) if it is possible to learn sequencing but I figured out that the answer is negative, maybe, because it is expensive and they do not want to take any chance. But I need something so that I can at least begin, then only I will get some experience. Does anyone know any workshops, or intern-ships etc which deal specifically with sequencing? I am not interested in library preparation, I just want that if someone gave me library, how should I load sample into the machine, how should I run it, how the output looks like continuously and what other things we have to do while running the machine and after running? It would be great to hear suggestions from people who do sequencing in their labs, how should we (bioinformaticians or others who want to learn) convince you? Or should I just concentrate on data analysis? Do you think its a bad idea to enter into 2 things at same time?

Thanks and best regards,

Vikas

[Khader Shameer]

I think this question is off-topic, any one agree with me to move this to forums ?

Answer 1

[Ido Tamir]

The important part for the researcher is the library generation. The other part: quality control of the library, cluster generation, loading the machine, preparing the solutions, checking running quality parameters, cleaning the machine etc.. is the work of specialised staff, done in a standardised way. This should be a black box for people outside of a sequencing facility. Messing one sample or a complete run up is very expensive. But I could imagine, that they might let you look at how they work.

The library generation however allows huge flexibility in experimental design and is something that I think one should know about at least theoretically. Regarding the possibilities it offers for innovative assays, or insertion of quality control measurements that help in evaluating the assays. I would rather go to a lab whose data you help to analyze and discuss hands-on stuff with them. Then the personal connection is also easier.

[Vikas Bansal]

Thanks. Yes I know about library preparation theoretically but I am more interested in running the machine. So there are no workshops etc specifically for this?

[Sean Davis]

I agree with Ido, here. We have MiSeq, Ion Torrent, Illumina GAII and HiSeq running in our lab. While running the machines is important, the library prep is where the real "science" is. I would encourage you to walk through loading the machines, etc., for learning sake, but running the machines is not something that folks do on a ad hoc basis.

[Vikas Bansal]

Thanks for your suggestion. But the thing is, my question is not regarding library prep. vs running machines. That is why, I already mentioned in question that I am not interested in lib prep practically. This is about my personal interest that I want to learn to run machines. Like, if some one gives me library and asks me to do sequencing, I would feel very happy if I will run the sample and give them their sequencing data.

[Sean Davis]

The training to run the machines typically is done by the instrument company at installation. After that, it would be done by the technician running the machine. There is not, to my knowledge, a course or workshop that teaches this.

Answer 2

[swbarnes2]

Going from library to a run is a very laborious process, and really not very scientifically interesting. With the exception of looking at the QC, there's really nothing about the process that would give you useful context about a run. These instruments are expensive, and runs usually last a week. Realisitically, no one is going to let you set up a run just because you are curious. Let the people who have been trained and who are practiced handle them. In 5 years, likely no one will be using those instruments anyway, so it's not like it's an important skill down the road.

[Vikas Bansal]

Thanks a lot for your answer. One comment - If I will consider that "in 5 years, likely no one will be using" (as you said) then I think there are lot of things I am not going to learn ;) . And who knows, may be, technology after 5 years will also last only for 4 - 5 years.

Answer 3

[Obi Griffith]

Cold Spring Harbor offers a two week course in Advanced Sequencing Technologies & Applications. Applications deadline for this year's course is July 15, 2012.

From their website: "This intensive 2 week course will explore applications of next generation sequencing technologies, with a focus on commercially available methods. Students will be instructed in the detailed operation of several revolutionary sequencing platforms, including sample preparation procedures, general data handling through pipelines, and in-depth data analysis. A diverse range of biological questions will be explored including DNA re-sequencing of human genomic regions (using cancer samples as a test case), de novo DNA sequencing of bacterial genomes, and the use of these technologies in studying small RNAs, among others. Guest lecturers will highlight their own applications of these revolutionary technologies."

[Vikas Bansal]

Thanks a lot Obi. This looks really good. I am definitely going to apply for this.