Vaccine Wars or not..

Attended a talk on ‘Vaccine Wars in the 21st Century’ by Dr. Gregory Poland from the Mayo Clinic at the University of Minnesota Rochester Campus

Major points Poland covered were on how we live in an age where information is confused with knowledge. Broadly he went over how the immunization rates are dropping and anti vaccine messages are being trumped. Quoting recent outbreak and the short story snippets behind them he covered diseases like measles and mumps. Stating that mistrust in people despite safe and effective vaccines was biased of, of emotions, heuristics and data they see.

Citing examples where the majority of audience failed to read an extra “in” in the phrase “Paris in in the spring” in a diamond shaped box among other tidbits of data and a simple math question of spending $1.10 where the bat costs exactly a $1 more than the ball – what could be the price of the ball 1c/5c/10c/20c, Poland justified how public (the audience in this case) messes up in understanding data.

He went on to cite examples of Andrew Wakefield and Jenny McCarthy regarding the measles vaccine and video hype of Desiree Jennings. He concluded the talk by pointing how people fail to see the data that they need to see to make ‘good’ decisions instead of getting vaccines for fear or by requirement/coercion.

Did the talk motivate the audience to spread the word about getting vaccines and being ‘good’ – that’s difficult to say. But the talk was certainly entertaining.

With so much information available, and I use the word information because what the general public sees is certainly not data. Interpreting data and getting information out of it is some hard work but forming a bead of knowledge from information is to each their own. Its difficult to say how a ‘vaccine war’ story unfolds – while you’re in the middle of it – the decision is solely yours, the end could work for you or totally not.

1000 Human Genome Project

The 1000 Genomes Project envisions to sequence genomes of a number of people from different populations and make this dataset publicly available to the scientific community as a comprehensive resource on human genetic variation. The project provides a thorough characterization of human genome sequence variation from the whole genomes sequences they have collected. This characterization of human genome sequence variation can be used as a foundation for further investigating the relationship between genotypes and respective phenotypes.

How this large a project works around the (still) high cost of deep sequencing whole genomes is interesting to note (Whole Genome Sequencing being: where multiple copies of the same genome are shred into pieces to be sequenced and then aligned with reference sequence to study variation in the sample compared to the reference sequence).

The 1000 Genome Project has chosen to take the route of “light sequencing” their collected whole genome sequences. This entails sequencing 4 copies of the genome, as they mention on their website 1000 Genomes at the same time and lowering the sequencing costs compared to deep sequencing methods. The project is designed in a manner where data across many samples will be combined to give efficient detection of most variants in the region of interest – and this explains that how in their point of view light sequencing of this large a data set seems more viable than deep sequencing a smaller data set. The Project also considers the detection of such variants to frequencies as low as 1%. Considering the large sample data combining data from this big a sample of whole genomes can give accurate insight into the variants and genotypes for each sample which might not have been as effective with light sequencing on a smaller sample.

After reading their project description we can deduce that this data set which has now from the original goal of sequencing the 1000 Human Genomes been expanded to sequencing 2500 genomes would provide useful information which can be useful for research studies where groups can study variations in large samples and deduce information with comparison to disease samples. Selection and population structure are among loads of interesting aspects that can be studied given the large amount of data sequencing has made available. Interesting.

My Genome is in yours!

A lot of ongoing discussion:
futurePundit
RazibKhan
GenomeWeb

But, the problem comes even before DNA!

If a person is diagnosed with a hereditary disease, then its easy to infer that family members are at higher risk, much the same way as a person having mutation X in the genome, likely that close relatives also do

So the whole point of dna sequence on the web gives up privacy is not the case, as whole diagnostic information using current methods also gives up the privacy

I think problem comes with the hype around dna sequencing, that it answers all the questions and one can make ‘accurate’ predictions using it… this makes the dna sequencing much more valuable than the existing diagnostic/phenotype information

Personal genomes projects

Planning to sequence 100s of individuals, PGP is a very exciting project that promises to bring loads of data, information and knowledge out to the public.

Their recent update talks about enrollments for the first 100 individuals who would be sequenced

PGP-100 Enrollment Update

The PGP has commenced the enrollment of the PGP-100. If you have submitted your enrollment materials but have not received an invitation, don’t worry – we will continue to send invitations for the PGP-100. We expect to begin enrollment for the PGP-1000 later this year.

Over the next several months we will be collecting tissue samples from as many PGP-100 participants as possible and data from the PGP-100 cohort should begin to arrive on the website shortly.

Moreover, there is a conference in April’10 getting a number of individuals with sequenced genomes on-stage. Sounds like an interesting ‘my genome has this, does yours‘ discussion!

PersonalGenomes.org is organizing a conference to be held in Boston on April 27, 2010. We’re calling it the GET Conference, which is short for Genomes, Environments, Traits.

The cost of personal genome sequencing continues to fall rapidly. While there are fewer than 25 individuals to-date with public genome sequences, we expect that number to climb sharply in the near future. By the midpoint of this decade, there may be 1 million or more individuals with complete genome sequences worldwide.

2010 is the last chance in history to bring a majority of the individuals with complete personal genome sequences together on the same stage to share their experiences and discuss the important ways in which personal genomes will affect key aspects of our lives. For the GET Conference 2010, we will be doing just that. Confirmed speakers, all of whom have been sequenced, include James Watson, Jay Flatley, Skip Gates, Esther Dyson, Stephen Quake, Misha Angrist, George Church, James Lupski, Dan Stoicescu, Seong-Jin Kim, Greg Lucier and Rosalynn Gill.

Proceeds from the conference will benefit PersonalGenomes.org – the non-profit organization supporting the Personal Genome Project and dedicated to serving as the global ambassador for emerging genomic technologies and knowledge that will positively impact the health and well-being of humankind. We hope to make the GET Conference an annual event where we bring together leading thinkers to discuss the impact of personal genomes on our lives, work and society.

We are offering the PGP community of supporters a special opportunity to receive a $250 discount off the registration price as a friend of the GET Conference. Register and use the discount code GETFRIEND to receive this pricing. Seating is limited to 200 people.

Register now, or visit the conference website: www.GETconference.org

For those unable to make it to Boston in April, we will be posting videos online after the conference.

Data collection, use and retention

I came across this interesting discussion and read about some very interesting facts on data privacy. Feel free to comment here, or use the links to join their discussion. A very relevant and related discussion is about the individual genomic data, and its privacy, a lot of which is already discussed by PGP

An international Consortium which is working on scientific-research project entitled “Promoting International Debate on Ethical Implications of Data collection, use and retention for Biometric and Medical Applications” is generating public debates on Ethical Implications of Biometric and Medical Data collection, use and retention. Questions for the discussion are posted at BioMedTalk.com and can be found by following this link http://www.biomedtalk.com/forumdisplay.php?f=617

Your participation in this debate are very and very welcome.

Also, Community will appreciate if you will disseminate this information among your colleagues, friends as well as students. So, please, pass this e-mail around your network to support debate.

To understand better how ethical aspects of Medical and Biometric data collection, use and retention can effect our everyday life please see these articles as an examples:

Emerging Issues: The Privacy of Medical Records

http://www.thedoctorwillseeyounow.com/content/bioethics/art1978.html

Disney has recorded onto tickets the geometry and shape of visitors’ fingers

http://newsinitiative.org/story/2006/09/01/walt_disney_world_the_governments

FBI wants instant access to British identity data

http://www.guardian.co.uk/uk/2008/jan/15/world.ukcrime

Visitors to Europe will face biometric screening and automated security checks

http://news.cnet.com/EC-plans-biometric-border-checks/2100-7348_3-6230775.html

So, please, visit discussion at BioMedTalk.com by following this link http://www.biomedtalk.com/forumdisplay.php?f=617
and post your replays to questions which you like.

ExomeSEQ: bringing reads on-target

It is surprising to look at some of the numbers from exome capture followed by sequencing projects.  The nature paper on exome-seq to identify cause of mendelian disorder has as low as 47% of uniquely mapping reads actually mapping on-target. Another study of 12 exome sequences also has a capture specificity of as low as 31%.

Why are these numbers so low?

Resources for Exome sequencing annotation

With the recent tsunami of sequencing data, and the reduced cost of whole exome capture technologies like Raindance, Agilent SureSelect and Nimblegen, a lot of data is bound to end up with Bioinformaticians. Annotating that data with information like coding variants, synonymous or not, etc is the first thing that needs to be done after mapping the reads and reporting variants in the sample.

3 tools seem to be all one needs for such an annotation – SIFT, SeattleSeqAnnotation and BEDTools. The first two are useful to obtain the annotation for a variant call, obtain allele frequencies for that, and generally filter the variants to a manageable list. They certainly have some overlap. BEDTools is a very useful suite to quickly merge and intersect mapped reads, variant calls, etc, with bed annotation files. It’s a single command to ‘intersect’ a bam alignment file with a bed annotation file to obtain all reads mapping on-target for a capture sequencing data.

There are of course some short-comings, and some more work to be done, so this place will be updated soon!

Twitter sequencing buzz

Getting louder with every base sequenced!

Searching for the keyword sequencing gives one this

The echoes from various corners are still audible for agbt that ended last month

There is a twitter group or twibe for next-gen sequencing

Some of the frequent tweeters whom I have got to following in the past week make sure the buzz never slows down

http://twitter.com/lukejostins

http://twitter.com/genomicslawyer

http://twitter.com/nutrigenomics

http://twitter.com/dgmacarthur

http://twitter.com/OmicsKnowmics

http://twitter.com/apfejes

http://twitter.com/BioInfo

http://twitter.com/thinkgenome

Changing Initial Username in UBUNTU

Change Initial Username in UBUNTU for a newer established account

Code:
sudo usermod –login NEWNAME –home /home/NEWNAME -m OLDNAME
sudo groupmod –new-name NEWGROUP OLDGROUP

OLDNAME is the current login name
NEWNAME is the desired login name

On a default ubuntu install,
OLDGROUP is the same as OLDNAME,
NEWGROUP is the same as NEWNAME

The “usermod” command will change the login name and move the home directory from /home/OLDNAME to /home/NEWNAME
And “groupmod” command will rename the old group name to the new group name, for permissions etc

Change Initial Username in UBUNTU for an older established account

If your OLDNAME is quite unique, one could follow up the “usermod” and “groupmod” commands with find command

Code:
find /home/NEWNAME/ -type f -name ‘*’ -exec sed -i ‘s/OLDNAME/NEWNAME/g’ {} \;

The “find” command will loop through every single file in /home/NEWNAME and change every occurrence of OLDNAME *within* the contents of the file to NEWNAME. This is an attempt to correct any mention of OLDNAME in your hidden configuration files, the .filename ones

The reason why this command is dangerous is because if your OLDNAME is something short like “igh” which is a substring of other words. If you try to change username “igh” to “may”, do not use the above command because any document that contains the word “right” would be changed to “rmayt”.
Be careful as terrible damage can be done with this find command

Trying the above commands is suggested only when you back-up first.

The other problem that sometimes occurs is that the .wine directory contains symlinks whose path contains the name OLDNAME.
(Things like this /home/NENWAME/.wine/drive_c/windows/profiles/OLDNAME/Desktop become broken symlinks).

Mostly these can be done manually, as they aren’t so many symlinks – I am assuming

Thanks to unutbu’s comments at Ubuntu Forums

Why Linux Why Ubuntu

Why Ubuntu is better than Windows or Is Windows 7 better than Ubuntu –

To each his own, Windows is an awesome OS for its ease of being already installed in most machines and to complement that we have polished software that works with it (and is easily available). And you need Windows to play games

So why linux?
Because its open source, can be modified to suit your needs and you can redistribute it without any keys to type in (i.e. CHEAP)
And the security linux provides is a lure.. let thou be lazy yet always safe. No anti viruses to install EVER..

And why Ubuntu?
Because it has a user-friendly GUI!
Talking ’bout cheap, it comes with an Office (Open Office), an email client (Evolution) all for free!
Don’t forget to throw in free applications which might not be as polished as those for Windows (considering Adobe Photoshop) But in all fairness not everyone purchases Photoshop for “fun”. So try GIMP!
Power up an old machine, and you have ubuntu running for you! Its compatible with more or less all hardware! And am not talking about graphics – you may not envision 3D stuff with that old a machine. Nonetheless your terminal works!

An amazing experience of trials and testing.. Hats off to Linux!