Tag Archives: sequencing

Molecular Biology 101: Synteny, Conservation and two wheat genomes

Somehow between going to the Netherlands, the Easter break, a week-long lab course and a conference talk to write I managed to miss not just one, but two really interesting, exciting and useful papers in Nature (Incidentally, I try not to write too much on here related to my PhD: I’m always a little scared that I’ll end up saying similar things about papers in my literature review and then being pulled up for plagiarism or something, but these are two interesting to miss.) But I digress.

Sequencing the wheat A and D genomes

Two weeks ago a consortium of Chinese and American scientists published two papers about sequencing both the A and the D genome progenitors for bread wheat. (Quick re-cap for the un-initiated. Wheat is a hexaploid i.e. instead of having one maternal and one paternal copy of each chromosome – that is, 2 in total, it has 3 pairs of each, making its genotype AABBDD). This is pretty big news for a couple of reasons: Continue reading

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Molecular Biology 101: A map from here to there (and the barley genome)

Barley and Wheat are pretty similar. After all they’re sisters… No really. In a flash of food-security related brilliance I named my guinea pigs Wheat and Barley. Let it never be said that I don’t take my PhD seriously…

But seriously: wheat and barley are both cereals; important food crops, important feed crops, vital for producing my two favourite beverages (20% of the worldwide narley yield goes for malting), not to mention bread… Wheat tends to get a lot more coverage though: the world grows around a quarter of the amount of barley that it does of wheat and the amount spent on barley-related science is therefore always likely to be a bit lower.  Continue reading

1092 humans, 14 populations, 1 map.

A little while ago, I wrote a tiny bit about the  1000 genomes project, in which scientists hoped to sequenced the genomes of 1000 individuals and use them as a basis of comparison to pin down the genetic variation contributing to disease. About a week ago, the consortium published their findings, and somehow I missed it: shock horror. Continue reading

100 genomes of 100 year olds for $100 000

On June 26th 2000 the consortium of researchers working on the Human Genome Project announced they had created their first ‘working draft’ of the human genome sequence. It had taken a decade to achieve, with groups in at least 5 countries collaborating, cost $3 billion and provided 7-fold coverage (i.e. on average, for any single point on the genome they had seven sequences).

Twelve years have gone by, and you might think that we would be busy sequencing other things. (Well, we sort of are: bonobosbananas…) But actually we’re still looking at human DNA. We might know what humans look like at a molecular level ‘on average’: but on average doesn’t tell you why some people are more prone to cancer, or why some people are more likely to get Alzheimers, or why some people can taste PROP. It doesn’t tell you why some people can live to 100 either, in spite of having genes that make them prone to clotting disorders or dementia or heart disease.

The competition

In 2006, non-profit organisation X-prize announced that they would give a $10 million prize to the company that could sequence (and assemble) the entire genomes of 100 centenarians at a cost of less than $1000 per genome in 30 days. With an unprecedented level of accuracy. Given the HGP cost around $3 billion to complete, that’s quite an ask!

The general idea is that by comparing these genomes, particular area of interest might ‘pop out’ as being associated with longevity. 100 people is actually a pretty small sample size, but it’s a starting point and may identify several candidate genes that can then be studied by other (cheaper!) methods.

The first entrant

For the first time, technology has progressed to a place where achieving the aims of the X prize really is a viable possibility. The Ion Proton sequencer (which, with a bit of luck, we’ll be buying soon-ish – squee!) might just be up to the job, and as of this week its inventors are the first company to actually sign up to the challenge. There’s still almost a year left for other companies to get on board, but Illumina (makers of the GA II and the new-to-the-market HiSeq) have already come out and said that they don’t plan to participate. Oxford Nanopore and Complete Genomics are still not making any decisions about whether or not to enter: presumably because they’re waiting  to see what state their technology is in 10 months from now.

As per the good old $1000 dollar genome, $10 000 analysis script, most of the time isn’t actually going to be spent sequencing the genomes. The vast majority of the 30 days will be spent in assembling the sequencing fragments into longer strings that match the known order of genes in the human chromosomes: the biggest time-constraint for the competitors is getting the sequencing done as fast as possible to leave the four whole weeks for genome assembly. We’ve been hearing for a while now that the $1000 dollar genome is right around the corner, so it’s exciting to see Ion Torrent putting their money where their mouth is. Come next October we can see whether they’re right.