| PMID |
|
|
| TITLE |
|
| Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan. |
|
| ABSTRACT |
|
|
|
| Multiple displacement amplification (MDA) has emerged as a promising new method of whole genome amplification (WGA) with the potential to generate virtually unlimited genome-equivalent DNA from only a small amount of seed DNA. To date, genome-wide high marker density assessments of MDA-DNA have focussed mainly upon suitability for single nucleotide polymorphism (SNP) genotyping applications. Suitability for short tandem repeat (STR) genotyping has not been investigated in great detail, despite their inherent instability during DNA replication, and the obvious challenge that this presents to WGA techniques. Here, we aimed to assess the applicability of MDA in STR genotyping by conducting a genome-wide scan of 768 STR markers for MDAs of 15 high quality genomic DNAs. We found that MDA genotyping call and accuracy rates were only marginally lower than for genomic DNA. Pooling of three replicate MDAs resulted in a small increase in both call rate and genotyping accuracy. We identified 34 STRs (4.4% of total markers) of which five essentially failed with MDA samples, and 29 of which showed elevated genotyping failures/discrepancies in the MDAs. We emphasise the importance of DNA and MDA quality checks, and the use of appropriate controls to identify problematic STR markers. |
|
| DATE PUBLISHED |
|
|
| HISTORY |
|
| PUBSTATUS |
PUBSTATUSDATE |
| pubmed |
2005/08/02 09:00 |
| medline |
2005/08/09 09:00 |
| entrez |
2005/08/02 09:00 |
|
| AUTHORS |
|
| NAME |
COLLECTIVENAME |
LASTNAME |
FORENAME |
INITIALS |
AFFILIATION |
AFFILIATIONINFO |
| Dickson PA |
|
Dickson |
Peter A |
PA |
|
Queensland Institute of Medical Research, Brisbane, 4029 Australia. |
| Montgomery GW |
|
Montgomery |
Grant W |
GW |
|
|
| Henders A |
|
Henders |
Anjali |
A |
|
|
| Campbell MJ |
|
Campbell |
Megan J |
MJ |
|
|
| Martin NG |
|
Martin |
Nicholas G |
NG |
|
|
| James MR |
|
James |
Michael R |
MR |
|
|
|
| INVESTIGATORS |
|
|
| JOURNAL |
|
| VOLUME: 33 |
| ISSUE: 13 |
| TITLE: Nucleic acids research |
| ISOABBREVIATION: Nucleic Acids Res. |
| YEAR: 2005 |
| MONTH: |
| DAY: |
| MEDLINEDATE: |
| SEASON: |
| CITEDMEDIUM: Internet |
| ISSN: 1362-4962 |
| ISSNTYPE: Electronic |
|
| MEDLINE JOURNAL |
|
| MEDLINETA: Nucleic Acids Res |
| COUNTRY: England |
| ISSNLINKING: 0305-1048 |
| NLMUNIQUEID: 0411011 |
|
| PUBLICATION TYPE |
|
| PUBLICATIONTYPE TEXT |
| Evaluation Studies |
| Journal Article |
| Research Support, N.I.H., Extramural |
| Research Support, Non-U.S. Gov't |
| Research Support, U.S. Gov't, P.H.S. |
|
| COMMENTS AND CORRECTIONS |
|
| REFTYPE |
REFSOURCE |
REFPMID |
NOTE |
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| Cites |
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|
| Cites |
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|
| Cites |
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12695328 |
|
|
| GRANTS |
|
| GRANTID |
AGENCY |
COUNTRY |
| AA007535 |
NIAAA NIH HHS |
United States |
| AA013320 |
NIAAA NIH HHS |
United States |
| AA013326 |
NIAAA NIH HHS |
United States |
| AA014041 |
NIAAA NIH HHS |
United States |
| AA07728 |
NIAAA NIH HHS |
United States |
| AA10249 |
NIAAA NIH HHS |
United States |
| AA11998 |
NIAAA NIH HHS |
United States |
|
| GENERAL NOTE |
|
|
| KEYWORDS |
|
|
| MESH HEADINGS |
|
| DESCRIPTORNAME |
QUALIFIERNAME |
| Female |
|
| Genetic Markers |
|
| Genome, Human |
|
| Genomics |
methods |
| Genotype |
methods |
| Humans |
methods |
| Male |
methods |
| Nucleic Acid Amplification Techniques |
methods |
| Tandem Repeat Sequences |
methods |
|
| SUPPLEMENTARY MESH |
|
|
| GENE SYMBOLS |
|
|
| CHEMICALS |
|
| REGISTRYNUMBER |
NAMEOFSUBSTANCE |
| 0 |
Genetic Markers |
|
| OTHER ID's |
|
| OTHERID |
SOURCE |
| PMC1182175 |
NLM |
|
