[Hplusroadmap] Fwd: My genome type donation.

[Dan Bolser]

On 28/02/2008, Bryan Bishop <kanzure at gmail.com> wrote:
> On Thursday 28 February 2008, Dan Bolser wrote:
>  > ---------- Forwarded message ----------
>  > From: jong bhak <jongbhak at yahoo.com>
>  > Date: 28 Feb 2008 09:19
>  > Subject: My genome type donation.
>  > To: dan.bolser at gmail.com
>  >
>  > Hi Dan,
>  >
>  > I have genome types for my son Subio and me.
>  > I donated them to genomics.org.
>  > http://genomics.org/index.php/Donate_your_genome
>  > I used http://decodeme.com for $985 USD each.
>  >
>  > You can have a look at:
>  > http://www.pnas.org/cgi/content/abstract/105/4/1176
>  >
>  > They seem to claim that they can sequence the whole genome within a
>  > day.
>  >
>  > Cheers
>  > Jong
>
>
> I took a look at the files (I have cached copies if anybody wants them).
>  For Jong Bhak here, the file looks something like this:
>
>  > Name,Variation,Chromosome,Position,Strand,YourCode
>  > rs4477212,A/G,1,72017,+,AA
>  > rs2185539,C/T,1,556738,+,--
>  > rs6681105,C/T,1,581938,+,TT
>  > rs11240767,C/T,1,718814,+,CC
>  > rs3094315,C/T,1,742429,-,TT
>  > rs3131972,C/T,1,742584,-,TT
>  ex: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3131972
>
>  Personally, I am more than amazed that decodeme gives you the actual
>  data files. That's a really, really good thing. Importantly, this is
>  the SNP dataset.
>
>  http://en.wikipedia.org/wiki/SNP_genotyping
>  > Genotyping provides a measurement of the genetic variation between
>  > members of a species. Single nucleotide polymorphisms (SNP) are the
>  > most common type of genetic variation. A SNP is a single base pair
>  > mutation at a specific locus, usually consisting of two alleles (where
>  > the rare allele frequency is ≥ 1%). SNPs are often found to be the
>  > etiology of many human diseases and are becoming of particular
>  > interest in pharmacogenetics. Because SNPs are evolutionarily
>  > conserved, they have been proposed as markers for use in quantitative
>  > trait loci (QTL) analysis and in association studies in place of
>  > microsatellites. The use of SNPs is being extended in the HapMap
>  > project, which is attempting to provide the minimal set of SNPs needed
>  > to genotype the human genome. SNPs can also provide a genetic
>  > fingerprint for use in identity testing (Rapley & Harbron 2004).
>
>  > In high density oligonucleotide SNP arrays, hundreds of thousands of
>  > probes are arrayed on a small chip, allowing for a large number of
>  > SNPs to be interrogated simultaneously (Rapley & Harbron 2004).
>  > Because SNP alleles only differ in one nucleotide and because it is
>  > difficult to achieve optimal hybridization conditions for all probes
>  > on the array, the target DNA has the potential to hybridize to
>  > mismatched probes. This is addressed somewhat by using several
>  > redundant probes to interrogate each SNP. Probes are designed to have
>  > the SNP site in several different locations as well as containing
>  > mismatches to the SNP allele. By comparing the differential amount of
>  > hybridization of the target DNA to each of these redundant probes, it
>  > is possible to determine specific homozygous and heterozygous alleles
>  > (Rapley & Harbron 2004). Although, oligonucleotide microarrays have a
>  > comparatively lower specificity and sensitivity, the scale of SNPs
>  > that can be interrogated is a major benefit. The Affymetrix Human SNP
>  > 5.0 GeneChip performs a genome-wide assay that can genotype over
>  > 500,000 human SNPs (Affymetrix 2007).
>
>  I'll release some notes soon enough on making an SNP arrayer. It looks
>  like this is just a giant oligonucleotide machine or microarraying
>  setup like in the videos on the biohack wiki. So it shouldn't be too
>  hard to document.
>
>  I would also be interested in creating a standard library of perl
>  scripts ( http://bioperl.org/ ) for interpreting this SNP CSVed
>  dataset, such as running it against the bioinformatics databases. Does
>  this dataset represent the entire human genome minus the common parts
>  throughout the population? So this is just based off of (1) predicting
>  where a change *should* be and (2) reading the nucleotides at that
>  point, right?

Don't know. I need to read more about and around 'decodeme.com' - its
an array based readout afaik, so it is focused on a certain set of
SNP's afaik.

The analysis of the 'sample user' on that site looks nice, but I'll
wager the details are not freely available. It would be really nice to
make some 'open' versions of these analysis so that people can feed in
their raw data and get a similar report for free.

I'll print some papers and drop the PDF's on the wiki when I get time.


Dan.

>
>  - Bryan
>  ________________________________________
>
> Bryan Bishop
>  http://heybryan.org/
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