Genomics

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 what did it really cost? Genome Technology asked J. Craig himself. In the October 2007 issue of GT, JCV estimates that the cost from the first Celera human genome project ( ... Read more
One of my readers asked: Why does genome sequencing cost so much? My short answer is because it's big. But I thought it would be fun to give a better answer to this question, especially since I'm sure many of you are wondering the same thing. Okay, so let's do some math. Don't worry, this math isn't very complicated and I'll explain where most of the numbers come from. Estimating costs from salaries First, we'll take the easy route. My experience with grant budgets has taught me that the greatest cost for any project comes from salaries. If ... Read more

If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. You may be wondering, and rightly so: just what is a SNP?

Never fear, hopefully this post will answer some of those questions.

SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a sequence of bases, and other people will have a different base at that position. The two forms of SNP are called "alleles." (Usually there are two forms, but that's ... Read more

"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 map, then slowly lifted his eyes and coldly surveyed his subject's beaming countenance. "You have an affinity for the ocean," said Holmes, "that you indulged to excess as a reckless youth. An experience as a medic in the military changed your ... Read more
I want my genome sequenced, too! Apparently, it's become a popular thing to get your genome sequenced. Craig Venter was the first. Jim Watson's genome (of Project Jim) was ceremonially released this morning (courtesy of 454), and now George Chuch, Larry King, cosmologist Stephen Hawking, Google co-founder Larry Page, Microsoft co-founder Paul Allen and former junk-bond trader Michael Milken want theirs done, too (1). Two articles from different GenomeWeb releases made a strange combination this morning when I turned on my computer. In one release, GW mentioned that NHGRI (the ... Read more
Is the case for open access truly "open and shut"? Will open access impede science by limiting genetic studies with families?

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Microsoft's brave new world The April ALPSP conference began with songs for the open access choir. Microsoft's Lee Dirks painted visions of a utopian future where everything will be open, labs shall be judged by the worthiness of their databases, and even scientists will learn to share. According to Dirks, "Open ... Read more

Shotgun sequencing. Sounds like fun. Speculations on the origin of the phrase I think that this term came from shotgun cloning. In the early days of gene cloning before cDNA, PCR, or electroporation; molecular biologists would break genomic DNA up into lots of smaller pieces, package DNA in lambda phage, transduce E. coli, and hope for the best. Consistent with the shotgun metaphor, we even used to store our microfuge tubes in plastic bullet boxes that my boss found at the sporting goods store. (Apparently this practice was unique ... Read more

Considering that several genomes that have been sequenced in the past decade, it seems amazing in retrospect, that the first complete bacterial genome sequence was only published 12 years ago (1). Now, the Genome database at the NCBI lists 450 complete microbial genomes (procaryotes and archea), 1476 genomes from eucaryotes, 2145 viruses, and genome sequences from ... Read more
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 technical details, there are some other genomic questions that you might like answered. How much does it cost to sequence a genome? I remember in 2002, when we were at the ... Read more
Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants? Two reports in Nature (1, 2) suggest that bacterial populations differ between people who are obese and people who not, and that the bacterial inhabitants of their guts, may be partly to blame. In one study, the authors studied the bacterial populations of their volunteers' intestines by compiling a data set of 18,348 DNA sequences for bacterial 16S ribosomal RNA by sampling feces. Wow! That's a lot of ... well, I won't say it, but you know what ... Read more

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