Researching SNPs (Phenylketonuria)

Summary

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Research SNPs

HGMD

HGMD (The Human Gene Mutation Database) is a human disease associated mutation database with a free and not current public version available for users from academic/nonprofit institutions. The database contains single base-pair substitutions in coding (missense, nonsense), regulatory and splicing-relevant regions of human nuclear genes, small deletions, small insertions and small combined insertions/deletions (indels), repeat expansions, gross deletions and gross insertions/duplications and complex rearrangements (including inversions). The information for mutations and polymorphisms is updated weekly <ref>http://www.hgmd.cf.ac.uk/docs/new_back.html, retrieved on July 22nd in year 2013</ref> and received by manual and computer-based search methods. For the optimization of the included data, online library screenings, PubMed and other freely available mutation databases are used. Silent mutations and not adequately analyzed or badly described mutations in the literature are excluded. <ref name="hgmd"> Peter D. Stenson, Matthew Mort, Edward V. Ball, Katy Howells, Andrew D. Phillips, Nick S. T. Thomas and David N. Cooper (2009): "The Human Gene Mutation Database: 2008 update". Genome Medicine 1: 13. doi:10.1186/gm13 </ref>

<figtable id="hgmd">

Mutation types for PAH found in HGMD with appendant quantity
Mutation type	# of mutations
Missense/nonsense	415
Splicing	82
Regulatory	1
Small deletions	66
Small insertions	8
Small indels	6
Gross deletions	27
Gross insertions/duplications	3
Complex rearrangements	1
Repeat variations	0 (no mutations)
Total Number of mutations: 609 (HGMD professional 2013.1: 720)

</figtable> 543 mutations of the table above are known for causing Phenylketonuria, 58 for Hyperphenylalaninaemia, one for Increased activity and one for association with Schizophrenia. For five of the mutations it is assumed that they cause Phenylketonuria and one Hyperphenylalaninanaemia.

dbSNP

dbSNP (Single Nucleotide Polymorphism ) is a freely available repository for short genetic variations. ... <ref name="dbsnp"> Elizabeth M. Smigielski, Karl Sirotkin, Minghong Ward and Stephen T. Sherry (2000): "dbSNP: a database of single nucleotide polymorphisms". Nucleic Acids Research Vol.28(1): 352-355. PubMed:10592272 </ref>

• What information is given?

The database includes basically single nucleotide substitutions (SNPs) however also a small number of microsatellite repeats and small insertion/deletion polymorphisms. <ref name="dbsnp"/>

• How recent?

dbSNP is updated after each new data submission. <ref name="dbsnp"/>

• Where does the information come from?

dbSNP gets the information from two different classes: firstly from original observations of sequence variation (submitted data) and the second one from content generated via computation on original submitted data (computed content)

SNPdbe

SNPdbe (nsSNP database of functional effects) ... <ref name="snpdbe"> Christian Schaefer, Alice Meier, Burkhard Rost and Yana Bromberg (2012): "SNPdbe: constructing an nsSNP functional impacts database". Bioinformatics Vol.28(4): 601-602. doi:10.1093/bioinformatics/btr705 </ref>

OMIM

OMIM (Online Mendelian Inheritance in Man) is a comprehensive, daily updated and online freely available knowledgebase of human genes and genetic disorders. An entry in OMIM includes the primary and sometimes alternative title and symbol, a gene map locus which displays the cytogenetic location of the gene or disorder, multiple map locations if a disease is known to be genetically heterogeneous, links to the NCBI’s ‘neighboring’ feature and several other informations and links to many useful genetic resources. Within the relevant gene entry allelic variants with functional significance are maintained. A few polymorphisms, associated with particular common disorders, are included as well. OMIM is particularly easy and uncomplicated for the use of the growing information in human genetics. The information is derived from biomedical literature and is written and edited at the John Hopkins University with input from scientists and physicians all over the world. <ref name="omim"> Ada Hamosh, Alan F Scott, Joanna S Amberger, Carol A Bocchini and Victor A McKusick (2005): "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders". Nucleic Acids Research Vol.33 (Database issue): D514-D517. doi:10.1093/nar/gki033, PubMed:15608251</ref>

SNPedia

SNPedia is a wiki resource, which ... <ref name="snpedia"> Michael Cariaso and Greg Lennon (2012): "SNPedia: a wiki supporting personal genome annotation, interpretation and analysis". Nucleic Acids Research Vol.40 (Database issue): D1308-D1312. doi:10.1093/nar/gkr798 </ref>

Mutation Map

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References

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