Saturday, 31 December 2011
However, as the author states at the end of his post "one can only imagine what we’ll know by next December, as large federally-funded initiatives ramp up their efforts to systematically apply exome and whole-genome sequencing to inherited disorders".
I'm sure everybody agrees that 2012 will be a very exciting year for Next Generation Sequencing and Personal Genomics.
It is thus not surprising to read in a recent article on PNAS that the "amount of copy number variation is four times that previously observed in other vertebrates, including humans". The authors of the study come to this conclusion after constructing a genome-wide, high-resolution CNV map comprising 6,080 CNV elements and encompassing 14.6% of the zebrafish reference genome. The analysis has been carried out using 80 zebrafish genomes, representing three commonly used laboratory strains and one native population.
Friday, 30 December 2011
This topic is reviewed in the recent Games with a scientific purpose article on Genome Biology:
"The scientific value of the Foldit system was first demonstrated by showing that game players could solve specific structure prediction problems. In the first major publication to discuss Foldit, Baker and colleagues (6) showed that game players could, in many cases, generate better structure predictions than the state-of-the-art Rosetta structure prediction program. Foldit then unleashed their army of folders on the task of solving the structure of the Mason-Pfizer monkey virus retroviral protease, a problem that was previously intractable to both computational and experimental methods (7). After 3 weeks of game play, the best solutions were screened and, remarkably, a solution to this previously unsolved structure was identified and subsequently validated. This achievement established Foldit as a legitimate resource for the structural biology community"
Zoran Popović, one of the founders of the Foldit project, has a audacious ambition for their community of game players: "Our ultimate goal is to have ordinary people play the game and eventually be candidates for winning the Nobel Prize".
Considering the enormous amount of data generated by NGS, and the importance of data curation, it won't be surprising to see a future for multiplayer online games in Personal Genomics.
"To detect differentially expressed genes under two conditions, statistical methods such as Poisson distributions are often used. However, to accurately detect differential expression of gene with low expression levels, more powerful statistical methods are desirable. In statistical literature, several methods have been proposed to compare two Poisson means (rates).
Through simulation study and real data analysis, the authors find that the Wald test with the data being log transformed is more powerful than other methods, including the likelihood ratio test, the variance stabilizing transformation test, the conditional exact test and the Fisher exact test.
When the count data in RNA-seq can be reasonably modelled as Poisson distribution, the Wald-Log test is more powerful and should be used to detect the differentially expressed genes."
Friday, 23 December 2011
This is a really good job, including scripts for manipulation and basic analysis on NGS and microarray data that will save you a lot of time and some headaches! Thanks for sharing!
Thursday, 22 December 2011
In their paper on exome techniques the authors have also compared SNVs detected with exome sequencing with those detected from a whole genome sequencing on the same sample. Results are quite interesting! They found that, considering the coding regions, a significant proportion of the identified variants (few thounsands) are different comparing WGS and WES data. In most cases this is explained by the fact that WGS cover some exon regions that capture kits simply miss meanwhile WES have a deeper coverage and so allows detection of variants in some regions which are low-covered with the whole genome sequencing. However a few hundred of variants remain that are uniquely identified by one of the two techniques...and this is quite away from expected...since one usually think that a WGS approach with adequate coverage will identify all the variants from a WES (plus of course many others located in the non-coding regions). Moreover about 300 SNVs that were identified by all three of the exome sequencing platforms but not by WGS are associated with human diseases, suggesting that exome sequencing can pick up variants with clinical relevance that WGS alone would miss.
"It was definitely surprising to me that the exome [sequencing] was finding information that the genome [sequencing] did not pick up," said Snyder. "Some of these are important regions — you can't just blow these off.". Given these results, it might make sense to do both WGS and exome sequencing "to make sure you are really covering your exome variants," he said. "If you can afford it, that's a good thing to do since you will get extra information from your exome that you would not have gotten from the genome."I post also an image from the original article that help visualizing this idea!
Wednesday, 21 December 2011
Tuesday, 20 December 2011
With the release of the draft sequence of the Neanderthal Genome, the questions about our evolution and our relationship with our bigger-body and bigger-brain cousins have gained new life. Comparative analysis have shown that the two Homo species are closer than previously supposed and that the two groups may have interbred before the Neanderthal extinction. The last studies in the field support the theory that less than 100,000 years ago Neanderthals and the ancestors of all non-African Homo sapiens lived side by side, and a few of them may have shacked up. So some of our ancestor may share Neanderthal DNA and some of us are more "Neanderthalian" than others...
What do you think about yourself? Do you feel like a big and smart H. neanderthalensis or just a common H. sapiens?
You may not be so interested, but Eric Durand, formerly at the Department of Integrative Biology at the University of California (Berkley) and now employed by 23andMe, took this question very seriously. He developed a bioinformatic tool to determine exactly how much Neanderthal is in you! This will definitely take the ancestry genetic test package offered by 23andMe to the ultimate level! As trivial as this could seem, the new interest in Neanderthal genetic testing has captured the attention of the Nature Blog, as you can read here.
Additional readings: Sleeping with the Enemy, The New Yorker; The Perfect Gift This Holiday Season: The Neanderthal Test, Discovery Magazine.
This was the first individual genome sequencing of a Mongolian, said Zhou Huanmin, project leader and head of the biological research lab at the Inner Mongolia Agricultural University. The results of this study are important for the detection of ethnicity-specific genome inheritances and the evolutionary features of Mongolians.
The the research team will continue to sequence the genomes of another 199 ethnic Mongolians and build a database consisting of Mongolian genetic code.
Monday, 19 December 2011
Unfortunately ordering from Italy you have to add $63.95 of shipping cost....
The GenomeWeb blog has a nice list for you:
Instead of Seven Lords A-Leaping, Try These | The Daily Scan | GenomeWeb
Thursday, 15 December 2011
Tuesday, 13 December 2011
Apparently is becoming more and more difficult to find skilled informatics professionals.
Sunday, 11 December 2011
You can select as a query either your gene of interest or a particular chromosomal region. The SNV data can be downloaded in either text or vcf format.
The goal of the NHLBI GO Exome Sequencing Project (ESP) "is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders". The study has been performed on European American and African American populations.