Got DNA sequencing problems? Who ya gonna call?

Why the ABRF of course!i-8b04187b7fb64bd408c576af1e9411ee-trace.gif

I spend a fair amount time every summer giving workshops for college and high-school teachers on genomics and bioinformatics. One of the things that always surprises them, is the amount of lab work that's carried out by people working in shared, or core lab facilities. For example, if I was working at a research university and I wanted to sequence some DNA, maybe several patient samples, or a bacterial genome, I would send the DNA to a core lab and they would send me the sequences. I would analyze the data and write the paper.

I've simplified that process a bit in my description, but that's more or less what happens.

Core labs work really well. You can provide access to expensive equipment that's maintained by a staff of knowledgeable people and the research can benefit from the economy of scale.

In the case of DNA sequencing there is certainly a benefit.

Some DNA samples are more troublesome than others.

Luckily, when you have a group of people with members who sequence 25,000 DNA samples a month, or more, you also have a wealth of experience and knowledge that's invaluable when you encounter that one strange sample.

I think the members of the Association for Biomedical Resource Facilities (ABRF) are well-known for their willingness to help. From poor quality DNA to mixed samples, to mysterious or missing primers, They've seen it all and are willing to share strategies for solving the problem.

One of the really nice things that's come out of this desire to help, is the DNA sequencing Research Group's guide to trouble-shooting sequencing problems.

Are your arrays behaving strangely? Do you have weird things happen after long stretches of the same base? Are your customers asking you to use new techniques for SNP detection?

The ABRF is the place to go.

More like this

These days, DNA sequencing happens in one of three ways. In the early days of DNA sequencing (like the 80's), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this. Then, in the 90's, genome centers came along. Genome centers are like giant…
Have you ever wondered how people actually go about sequencing a genome? If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are Phred, Phrap, and Consed?…
About a week ago, I offered to answer questions about subjects that I've either worked with, studied or taught. I haven't had many questions yet, but I can certainly answer the ones I've had so far. Today, I'll answer the first question: How do you sequence a genome? Before we get into the…
A couple of years ago, I answered a reader's question about the cost of genome sequencing. One of my readers had asked why the cost of sequencing a human genome was so high. At that time, I used some of the prices advertised by core labs on the web and the reported coverage to estimate the cost…