Search tips
Search criteria

Results 1-2 (2)

Clipboard (0)

Select a Filter Below

more »
Year of Publication
Document Types
1.  Automatic extraction of mutations from Medline and cross-validation with OMIM 
Nucleic Acids Research  2004;32(1):135-142.
Mutations help us to understand the molecular origins of diseases. Researchers, therefore, both publish and seek disease-relevant mutations in public databases and in scientific literature, e.g. Medline. The retrieval tends to be time-consuming and incomplete. Automated screening of the literature is more efficient. We developed extraction methods (called MEMA) that scan Medline abstracts for mutations. MEMA identified 24 351 singleton mutations in conjunction with a HUGO gene name out of 16 728 abstracts. From a sample of 100 abstracts we estimated the recall for the identification of mutation–gene pairs to 35% at a precision of 93%. Recall for the mutation detection alone was >67% with a precision rate of >96%. This shows that our system produces reliable data. The subset consisting of protein sequence mutations (PSMs) from MEMA was compared to the entries in OMIM (20 503 entries versus 6699, respectively). We found 1826 PSM–gene pairs to be in common to both datasets (cross-validated). This is 27% of all PSM–gene pairs in OMIM and 91% of those pairs from OMIM which co-occur in at least one Medline abstract. We conclude that Medline covers a large portion of the mutations known to OMIM. Another large portion could be artificially produced mutations from mutagenesis experiments. Access to the database of extracted mutation–gene pairs is available through the web pages of the EBI (refer to
PMCID: PMC373272  PMID: 14704350
2.  SNP genotyping on a genome-wide amplified DOP-PCR template 
Nucleic Acids Research  2002;30(22):e125.
With the increasing demand for higher throughput single nucleotide polymorphism (SNP) genotyping, the quantity of genomic DNA often falls short of the number of assays required. We investigated the use of degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) to generate a template for our SNP genotyping methodology of fluorescence polarization template-directed dye-terminator incorporation detection. DOP-PCR employs a degenerate primer (5′-CCGACTCGAGNNNNNNATGTGG-3′) to produce non-specific uniform amplification of DNA. This approach has been successfully applied to microsatellite genotyping. We compared genotyping of DOP-PCR-amplified genomic DNA to genomic DNA as a template. Results were analyzed with respect to feasibility, allele loss of alleles, genotyping accuracy and storage conditions in a high-throughput genotyping environment. DOP-PCR yielded overall satisfactory results, with a certain loss in accuracy and quality of the genotype assignments. Accuracy and quality of genotypes generated from the DOP-PCR template also depended on storage conditions. Adding carrier DNA to a final concentration of 10 ng/µl improved results. In conclusion, we have successfully used DOP-PCR to amplify our genomic DNA collection for subsequent SNP genotyping as a standard process.
PMCID: PMC137182  PMID: 12434007

Results 1-2 (2)