Difference between revisions of "Researching SNPs (PKU)"

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===Distributin of Mutations===
<figtable id="tab:mutation_distri">
<caption>Distribution of SNPs from different databases on the PAH gene.</caption>
{| style="border-style: solid; border-width: 1px"
|[[File:Hgmd_distribution.jpg|200px|thumb|left|Distribution of SNPs from HGMD on the PAH gene.]]
|[[File:SNPdbe_distribution.jpg|200px|thumb|left|Distribution of SNPs from SNPdbe on the PAH gene.]]
|[[File:DbSNP_distribution.jpg|200px|thumb|left|Distribution of SNPs from dbSNP on the PAH gene.]]
|[[File:DbSNP_missense_distribution.jpg|200px|thumb|left|Distribution of missense SNPs from dbSNP on the PAH gene.]]
|[[File:DbSNP_silent_distribution.jpg|200px|thumb|left|Distribution of silent SNPs from dbSNP on the PAH gene.]]

Revision as of 21:54, 9 June 2012

Mutants walk the earth.

There are mutants on your block. There's a mutant right next door. There's one in your shoes.

We are, face it, all mutants. Humanity amounts to a string of mutations millennia-old, tweaks that gave us an edge over the next brute down the line. Upright posture; opposable thumb; prefrontal lobes.

The all-time specifically human thing is language. Familiar yet mysterious, language is the angelic part of us angel/beasts. It is spiritual, evanescent, fugitive - even gorgeous words like those have an unearthly shimmer. - from philly.com

Short Task Description

In this weeks task, we will research SNPs in the PAH gene that cause or do not cause a different phenotype of the phenylalanine hydroxylase. The chosen databases are: The public release of the Human Gene Mutation Database (HGMD), dbSNP, SNPdbe, OMIM and SNPedia. You may find a detailed task description here. A very dense journal, which offers only a small overview over the things we did can be found here.



<figtable id="tab:modelling_scores"> Key Values of the different SNP databases

Database Last Update Number of Entries Number of Entries concerning PAH Type of information Sources Curation/Verification Comment
HGMD public after 3 years (quarterly updated) 50,129 (only mis-/nonsense) 397 (only mis-/nonsense) all types of mutations current literature manual and computerised search in current literature too much advertising
dbSNP Oct 2011 292,031,791 2590 SNPs, short in/dels, polymorphisms, others submitted by registered sources (labs, institutes,.. ) clustering of identical submissions by NCBI
SNPdbe Mar 2012 1,691,464 328 nonsyn. SNPs Swissprot, dbSNP, PMD, OMIM, 1000 genomes cf. sources Predictions of functional effect, experimental evidence if available in source
OMIM June 2012 21,257 (Summary entries) 1 (64 selected SNPs) catalog of human genes and genetic disorders and traits current literature manually curated
SNPedia continuous, Wiki-style 29,058 53 SNPs publicly edited publicly edited get genotyped and predicted


Distributin of Mutations

<figtable id="tab:mutation_distri"> Distribution of SNPs from different databases on the PAH gene.

Distribution of SNPs from HGMD on the PAH gene.
Distribution of SNPs from SNPdbe on the PAH gene.
Distribution of SNPs from dbSNP on the PAH gene.
Distribution of missense SNPs from dbSNP on the PAH gene.
Distribution of silent SNPs from dbSNP on the PAH gene.






29 synonymous SNPs



use to annotate common variants/interesting SNPs (e.g. .0002)



Following the task description, we looked at the conservation score, to determine quickly, whether a mutation found here is disease causing or not. Our reasoning can be found at this subpage.



The SNPs concerning PAH in SNPedia all appear in dbSNP and there is no additional information attached so we do not investigate them in any separate way.


<figure id="fig:SNPMapping">

Mapping of SNP entries found in the different databases. The bar on the left symbolizes the sequence of the PAH-gene. Every horizontal line refers to at least one entry from any of the databases. The numbers on the left of the bar refer to their amino acid position. Colorcoding in the middle section which contains the different mutations:
red: disease causing according to HGMD
orange: missense, but no entry in HGMD
green: silent mutation
Colorcoding in the last column of the picture is for better overview and is according to the meaning of the effect from SNPdbe:
red: probably disease causing
green: probably not disease causing