Researching SNPs TSD
Oh it was gorgeousness and gorgeosity made flesh. The trombones crunched redgold under my bed, and behind my gulliver the trumpets three-wise silverflamed, and there by the door the timps rolling through my guts and out again crunched like candy thunder. Oh, it was wonder of wonders. And then, a bird of like rarest spun heavenmetal, or like silvery wine flowing in a spaceship, gravity all nonsense now, came the violin solo above all the other strings, and those strings were like a cage of silk round my bed. Then flute and oboe bored, like worms of like platinum, into the thick thick toffee gold and silver. I was in such bliss, my brothers.
-A Clockwork Orange
The journal for this task can be found here.
- 1 Sequence mapping
- 2 Mutations
- 3 HGMD
- 4 dbSNP
- 5 SNPdbe
- 6 OMIM
- 7 SNPedia
- 8 Mutation map
- 9 Conclusion
- 10 References
The different databases use different sequences as basis for the indices of their SNP data. In the following, the reference protein sequence remains P06865, however all databases base their annotations on nucleotide sequences as well. While the final annotations will only be displayed mapped onto the protein sequence, NM_000520.4 will be used as a nucleotide reference sequence in the background. This entry describes an mRNA of HEXA and is also linked to by the Uniprot entry of P06865.
HGMD lists NM_000520.3 as reference, which is a previous version of NM_000520.4 that was chosen as reference for this task. A Needleman-Wunsch pairwise sequence alignment between the two nucleotide sequences in the entries shows that there are two single nucleotide differences in the last third of the sequence and that the more current version of the entry is 117 nucleotides longer at the beginning of the sequence. Since this region is annotated to belong to an exon, the question remains whether this has an effect on the protein sequence. A short comparison shows that there is a single differing residue at position 436 where a Val in NM_000520.3 is subsituted by an Ile in NM_000520.4. However since HGMD does not list a SNP at this position, this is not an issue.
A table here?, with the different reference sequences per database? snpdbe has a lot tough!
ADD dbSNP! do they alle use the .04 one? (and say snpedia is the same more or less, because...) TODO
For an examination of the biologic mechanism Tay-sachs disease the genetic differences are considered to be important to view on protein and not an DNA level. Therefore all SNPs were extracted for the Uniprot sequence of P06865. Mutations are described by the simple scheme of [WT_AA][POS][MT_AA]. Nonsense mutations were ignored, if present in the database at all, since it would not make sense to predict an effect for these in the following tasks.
The Human Gene Mutation Database (HGMD) <ref name="hgmd">Stenson,P.D. et al. (2009) The Human Gene Mutation Database: 2008 update. Genome medicine, 1, 13.</ref> is freely available to non-profit organisations and academic users. This free version is updated with a delay of three years after inclusion in the database <ref name="hgmd_inclusiondelay">http://www.hgmd.cf.ac.uk/docs/disclaimer.html</ref>. Indeed the most recent mutation linked to HEXA was published in 2008. However in the whole database there seems to be a small number of entries with publication dates from 2010 to 2012 that are also available in the free version <ref name="hgmd_statistics">http://www.hgmd.cf.ac.uk/ac/hahaha.php</ref>, the exact mechanism is therefore not entirely clear.
HGMD is updated semi-automatically, amognst others, by screening the PubMed database. In contrast to other databases like dbSNP the same mutation is only recorded once and attributed to the publication that first mentioned it <ref name="hgmd"/>. The entries are not limited to SNPs but also include splice site changes, small and larger insertions and deletions as well as changes affecting regulation and complex rearrangements like inversions. Synonymous SNPs however are not recorded <ref name="hgmd"/>.
Currently HGMD contains 88745 entries.
A 3-day trial for the professional version of HGMD has been requested and has by now been received. In the following the more recent data of the professional version will be used and at some points, compare to the data available from the free version.
HGMD has a distinct subsite for HEXA and its missense/nonsense mutations. After exclusion of all nonsense mutations, 60 SNPs remain in the free version and 65 in the professional version. As to be expected, the five new entries are based on publications from 2009-2011. At the specific sites 58, 207, 259, 322 and 497, no other mutations have been known so far, making this highly valuable information. In addition three of these mutations are not found in any other database, while the most recent one C58Y is present in OMIM as well and Y497C from 2009 can also be found in dbSNP and snpdbe.
The Single Nucleotide Polymorphism Database dbSNP stores information on diverse DNA variations such as single base nucleotide substitutions and short deletion and insertion polymorphisms <ref name="dbsnpp">Wheeler DL, Barrett T, Benson DA, et al. (January 2007). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Res. 35 (Database issue): D5–12. DOI:10.1093/nar/gkl1031 </ref>. There are neutral polymorphisms, polymorphisms corresponding to known phenotypes, and regions of no variation. This is also integrated with other NCBI genomic data. It was established by the National Center for Biotechnology Information and is now available as build 135 with a last update on Oct 2011. The database is designed to accept new submissions also in a large batch format. Up to now it consists of 292,031,791 submissions <ref name="dbSNPsummary"> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi </ref>.
A search for all mutations reveals 579 entries in the form of rs IDs. Some rs IDs are obsolete and redundant thus there are 526 unique and up to date SNPs alltogether for HEXA in homo sapiens. 406 of those are in an intron region, 14 mRNA utr, 14 nonsense or stop gained. There are 18 unique non-synonymous mutations and 51 unique missense mutations. What kind of mutations the remaining 23 entries are remains unclear.
SNPdbe is a database of non-synonymous SNPs in the form of single amino acid substitutions (SAASs). It combines the data from dbSNP, SwissProt (including SwissVar), PMD and 1000 genomes. This webinterface was designed to provide combined annotation of experimentally derived functional and structural impact, predicted functional effect, associated disease, average heterozygosity, experimental evidence of the nsSNP and evolutionary conservation. The database currently holds 1,691,464 entries and was last updated in March 2012 <ref name="snpdbe"> C Schaefer, A Meier, B Rost, Y Bromberg (2012). SNPdbe: Constructing an nsSNP functional impacts database.Bioinformatics 28(4):601-602.</ref>.
Hex A mutations
The search for hexosaminidase A in human yields 76 entries. Of those 55 are present in dbSNP with protein identifier NP_000511 and 21 are solely from Swissprot or SwissVar with the accession number P06865. 18 snps are experimentally validated, see <xr id="snpdbeexp"/>. <xr id="snpdbecons"/> show the distribution of the conservation of wildtype and mutant amino acids. 15 snps have a higher conservation of the wildtype than 50%. The mutant conservation does not exceed 15%.
OMIM, the Online Mendelian Inheritance in Man, provides comprehensive and referenced information on human genes and genetic phenotypes. It catalogs genetic disorders with collected details on the corresponding genetic locations <ref name="omimpaper">Hamosh, A.; Scott, A.; Amberger, J.; Bocchini, C.; McKusick, V. (2004). "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders". Nucleic Acids Research 33 (Database issue): D514–D517.</ref>. OMIM is stated to be updated daily. Up to now it is comprised of 21,266 entries. The entries aim at offering a multitude of external links to other genetic resources<ref name="omomwebsite">http://www.omim.org/</ref>.
OMIM contains a dedicated subsite for HEXA <ref name="omim_hexa">http://omim.org/allelicVariant/606869</ref> which lists 58 variants in total. Among these are entries that can be mapped to 36 unique rs-identifiers. After exclusion of all variants that are neither missense nor synonymous, 29 missense and 1 synonymous variation remain. All of these were already found by querying dbSNP.
Additionally, there are 19 entries that do not contain cross-references to dbSNP. Of these 18 are deletions, insertions or intronic variants, all of which are not relevant for this task. One mutation however, Cys58Tyr has to be added to the 29 missense mutations from above. Interestingly this mutation is not present in any of the other databases. The original publication <ref name="Najmabadi2011">Najmabadi,H. et al. (2011) Deep sequencing reveals 50 novel genes for recessive cognitive disorders. Nature, 478, 57-63.</ref> lists this mutation in connection with a phenotype of mild Tay-Sachs disease. A reason that this entry is missing from all other databases might be the fairly new publication date. It would be interesting to see if it is among the 6 additional variants available in HGMD Professional.
SNPedia is a freely available wiki-based database of SNPs <ref name="snpedia">http://en.wikipedia.org/wiki/SNPedia (since SNPedia references this article themselves (http://www.snpedia.com/index.php/SNPedia:FAQ#What_is_SNPedia.3F) Wikipedia will be accepted as a citation)</ref>. The bulk of information are entries crosslinked to dbSNP via Rs-Identifiers, therefore anything in dbSNP can potentially be present in SNPedia as well. In addition there are pages for identifiers from 23andMe <ref name="23andme">https://www.23andme.com/</ref>, haplotypes and even pages describing information gained from complete genomes of specific people <ref name="snpedia_faq_onlysnps">http://www.snpedia.com/index.php/SNPedia:FAQ#SNPs_only.3F_what_about_CNVs.2C_indels.2C_inversions.2C_epigenetics_..._.3F</ref>.
Due to the nature of the wiki system every user is able to add information at any time. In addition, periodic updates based on text-mining are fed into the database as well <ref name="snpedia_nar">Cariaso,M. and Lennon,G. (2012) SNPedia: a wiki supporting personal genome annotation, interpretation and analysis. Nucleic acids research, 40, D1308-12.</ref>. Quality of the data is ensured on the hand by manual curation of users and editors and on the other hand by automated external programs that check for inconsistencies or missing information on a regular basis <ref name="snpedia_nar"/>.
At the time of writing SNPedia claims to contain 29135 SNPs <ref name="snpedia_faq_howmany">http://www.snpedia.com/index.php/SNPedia:FAQ#How_many_SNPs_are_in_SNPedia.3F</ref>, however this number was last update in August 2011 <ref name="snpedia_faq_history">http://www.snpedia.com/index.php?title=SNPedia:FAQ&action=history</ref>. Given the previous trends <ref name="snpedia_nar"/> it number should have significantly increased by now.
SNPedia does contain a dedicated subpage for TSD, however only few SNPs are listed there. More importantly SNPedia does not contain a dedicated page for HEXA. Therefore SNPs were searched with the query 'Gene = HEXA'. This results in 36 entries, most of which were last updated in Februrary 2012 by the automated SNPediaBot. One entry (Rs28940871) contains additional, user added information, all others are empty apart from the cross-references to other databases. During retrieveal one entry was already excluded, since it did not contain information of the change on the protein level in dbSNP. Additionally 6 more entries were excluded because they described neither missense nor synonymous mutations. There final set of SNPs from SNPedia therefore consists of 29 missense mutations and one synonymous mutation, all of which are also contained in the SNPs that were retrieved directly from dbSNP <ref name"snpedia_dbsnp_intersection">Intersection SNPedia and dbSNP</ref>.
The overlap between all databases with the free version of HGMD can be viewed here.
<figtable id="tbl:Overlapping SNPs">
|HGMD, dbSNP, SNPdbe, SNPedia, OMIM||29||F211S R247W S210F L39R W485R R499C R170W W474C D258H M1V R504C G454S E482K R499H G269S Y180H M301R R178H W420C R178L R170Q R504H L451V V200M H204R G250D K197T L127R R178C|
|HGMD, dbSNP, SNPdbe||3||S4P Y497C R249W|
|dbSNP, SNPdbe, SNPedia||1||I436V|
|HGMD, SNPdbe||16||R252H S226F S279P C458Y N196S V192L R252L V391M G455R G269D I335F D314V G250S P25S L127F R166G|
|dbSNP, SNPdbe||19||E214D S293I S279C L11P V376G I389T L183H N399D N43D P182L Q35P A13V Q45P P81A A410V A479T E506D S59L G343V|
|HGMD||16||A246T M1L L484P R249Q G250V D465N G454D Y37N W203G I388M F300L D322G D207E T259A M1T Q374R|
|SNPdbe||8||N295Q N157Q N115Q S331P L484Q A418G N295S F434L|
TODO alice add somewhere dbSNP and snpdbe (rate your own work, woho!) ...hm well maybe I dont want to rate snpdbe so much I can to snpedia somehow or we leave it out because we're biased :P but you have to do dbsnp
SNPedia's wiki system can in theory be very powerful, however for HEXA only a single entry contained additional information added by a human. Unfortunately the number of active users currently seems to be very low, limiting the possibilities that lie within the system <ref name="snpedia_active_users">http://www.snpedia.com/index.php/Special:Statistics</ref>. The lack of further information cannot be complemented by the SNPs present, because all of them can be found in dbSNP as well. On the other hand, OMIM also has very similar data and only one unique entry, that is not present in any of the other databases. However OMIM contains a text with a summary and additional information for every entry. So while SNPedia might have the foundation to become superior through crowd-sourcing, currently the more closed system OMIM seems clearly better.
HGMD has contained the largest number of missense SNPs, drawbacks however are the closed system, that makes retrieval of the data harder than necessary and direct programmatic access to data virtually impossible without paying for the service. For research based on single genes of interest this is not an issue though.