Biomedical Engineering Reference
In-Depth Information
by these advances have reliably identified many novel genomic locations associated with
complex diseases [6].
Only rarely do the SNPs used to identify these loci prove to be the causal variants
themselves. The vast majority of SNPs, in fact, are believed to be phenotypically neutral.
Regions identified by association studies must be exhaustively screened to identify all DNA
sequence variants before the complete genotype - phenotype relationship can be understood.
Targeted DNA resequencing on capillary-based platforms (such as the ABI 3730XL) remains
the gold standard for exhaustive variant discovery across a specific region of interest.
2.2 Methods and approaches
2.2.1 Repositories of known genetic variants
For humans and many other organisms, public databases contain a substantial number of
SNPs and other sequence variants. The central repository for genetic variants is dbSNP [1],
Table 2.1
Organisms with more than 1000 reference
SNPs in public database dbSNP (build 129) [7].
Organism
SNPs
Homo sapiens
14 708 752
Mus musculus
14 380 528
Gallus gallus
3 293 383
Oryza sativa
5 418 373
Canis familiaris
3 301 322
Pan troglodytes
1 543 208
Bos taurus
2 223 033
Monodelphis domestica
1 194 131
Anopheles gambiae
1 131 534
Apis mellifera
1 117 049
Danio rerio
662 322
Felis catus
327 037
Plasmodium falciparum
185 071
Rattus norvegicus
43 628
Saccharum hybrid cultivar
42 853
Sus scrofa
8427
Ovis aries
4181
Bos indicus
×
Bos taurus
2484
Macaca mulatta
780
Caenorhabditis elegans
1065
