Getting an accurate genome sequence requires that you collect the data at least twice argue Robasky, Lewis, and Church in their recent opinion piece in Nat. Rev. Genetics [1]. The DNA sequencing world kicked off 2014 with an audacious start.
Previously, I introduced the idea that the $1000 genome has not been achieved because it is defined in simplistic terms that ignore many aspects of data completeness and verification. In that analysis, I cited a recent perspective by Robasky, Lewis, and Church [1] to present concepts related ...
In our series on why $1000 genomes cost $2000, I raised the issue that the $1000 genome is a value based on simplistic calculations that do not account for the costs of confirming the results. Next, I discussed how errors are a natural occurrence of the many processing steps required ...
In our series on why $1000 genomes cost $2000, I raised the issue that the $1000 genome is a value based on simplistic calculations that do not account for the costs of confirming the results. Next, I discussed how errors are a natural result of the many ...
A few weeks back, we published a review about the development and role of the human reference genome. A key point of the reference genome is that it is not a single sequence. Instead it is an assembly of consensus sequences that are designed to deal with variation in the ...
I know some of you enjoy looking at data and seeing if you can figure out what's going on. For this Friday's puzzler, I'm going to send you to FinchTalk, our company blog, to take a look at lots of data from a resequencing experiment that was done to look ...
What happens when high school students clone and sequence genomic DNA? Background DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will ...
This the second part of three part case study where we see what happens when high school students clone and sequence genomic plant DNA. In this part, we do a bit of forensics to see how well their sequencing worked and to see if we can anything that could help ...
This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes ...
A few days ago, I wrote about a cool project that some high school students did where they used DNA sequencing to identify seafood. One question that came up from one of my commenters was how a school would start a project like this. I'm totally biased, but I think ...
One of my colleagues has a two part series on FinchTalk (starting today) that discusses uncertainty in measurement and what that uncertainty means for the present and Next Generation DNA sequencing technologies. I've been running into this uncertainty myself lately. I have always known that DNA sequencing errors occur. This ...
In simple Mendelian genetics, a single change in one gene can produce a large change in mortality. The National Human Genome Research Institute (NHGRI) will be funding genomics studies on Mendelian traits using a similar strategy. NHGRI will fund a small number of centers, dominant centers you might say, and ...
Two teenagers, Kate Stoeckle and Louisa Strauss, carried out their own science project over the past year. They visited 4 restaurants and 10 grocery stores and gathered 60 samples of fish and sent them off to the University of Guelph to get sequenced. I like this story. One of my ...
Which read(s): 1. contain either a SNP (a single nucleotide polymorphism) or a position where different members of a multi-gene family have a different base? C 2. doesn't have any DNA? B 3. is a PCR product? A, B, and C. All of three reads were obtained by sequencing PCR ...
Since DNA diagnostics companies seem to be sprouting like mushrooms after the rain, it seemed like a good time to talk about how DNA testing companies decipher meaning from the tests they perform. Last week, I wrote about interpreting DNA sequence traces and the kind of work that a data ...
You might think the coolest thing about the Next Generation DNA Sequencing technologies is that we can use them to sequence long-dead mammoths, entire populations of microbes, or bits of bone from Neanderthals. But you would be wrong. Sure, those are all cool things to do, but Next Generation DNA ...
I had the good fortune on Thursday to hear a fascinating talk on deep transcriptome analysis by Chris Mason, Assistant Professor, at the Institute for Computational Biomedicine at Cornell University. Several intriguing observations were presented during the talk. I'll present the key points first and then discuss the data. These ...
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many ...
Genome Web's Daily Scan noted an interesting blog post today from John D. Halamka, one of the people to get his genome sequenced through the personal genome project. I was interested to see his post since Genome Web wrote that he was discussing data standards and we have been writing ...
Scale, proportion, and quantity belong to one of the cross cutting concepts in the next generation science standards (NGSS). According to Volume 2 of the NGSS, "in engineering, no structure could be conceived much less constructed without the engineer's precise sense of scale." The authors go on to note that scale and proportion are best understood using the scientific practice of working with models.
Scale, proportion, and quantity belong to one of the cross cutting concepts in the next generation science standards (NGSS). According to Volume 2 of the NGSS, "in engineering, no structure could be conceived much less constructed without the engineer's precise sense of scale." The authors go on to note that ...
A few weeks ago, I did some "back-of-the-envelope" calculations to explain to a reader why genome sequencing costs so much. I estimated that, if JCV's genome were sequenced at the cost advertised by university core laboratories, his genome would cost about $128 million. That was an estimate, of course. But ...
" Come quickly, Watson," said Sherlock Holmes, " I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend." The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value. Holmes gazed thoughtfully at the ...
One of the interesting things I learned today was that many people are calling for the genome sequences of the chimps and Macaques to be finished. This is especially amusing because the human genome isn't quite done. We're primates, too! Why not finish our genome? [I blame these new-found revelations ...
