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Erhart MA, Kim T, Crews GM, Pandya A. The use of unilateral PCR to identify prominent heteroduplexes formed during PCR of the mouse microsatellite locus D17Mit23. Mol Biotechnol 2006; 33:37-48. [PMID: 16691005 DOI: 10.1385/mb:33:1:37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 05/09/2023]
Abstract
Microsatellite markers are useful tools for understanding the evolutionary history of discrete segments of the mammalian genome. We used the microsatellite marker D17Mit23 to study the portion of the mouse genome known as the t complex, a naturally occurring variant of Chromosome 17. We identified an allelic variant of D17Mit23, which is shared by two forms of the t complex, the t haplotypes t(w2) and t(Lub2). Polymerase chain reaction (PCR) analysis of DNA samples from mice that were heterozygous for either t haplotype resulted in gel patterns with prominent bands of higher molecular weight in addition to the bona-fide D17Mit23 alleles. The appearance of these higher molecular weight bands, although consistent with heteroduplex formation, was not diminished through the use of reconditioning PCR. We used a modified form of asymmetric PCR, called "unilateral PCR," to show that the higher molecular weight bands are heteroduplexes and to identify their constituent strands. Certain microsatellite motifs may be especially prone to the production of prominent heteroduplex products, and this may lead to the erroneous genotyping of DNA samples.
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Affiliation(s)
- Mark A Erhart
- Department of Biological Sciences, Chicago State University, 9501 S. King Drive, Chicago, IL 60628, USA.
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McCallum M, Baker C, Gillespie K, Cohen B, Stewart H, Leonard R, Cameron D, Leake R, Paxton J, Robertson A, Purdie C, Gould A, Steel M. A prognostic index for operable, node-negative breast cancer. Br J Cancer 2004; 90:1933-41. [PMID: 15138474 PMCID: PMC2409476 DOI: 10.1038/sj.bjc.6601826] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Clinical data and samples from patients diagnosed, more than 10 years previously, with operable node-negative breast cancer (participants in the Scottish Adjuvant Tamoxifen trial), were revisited. Cases with two distinct categories of outcome were selected; more than 10 years disease-free survival ('good outcome') or distant relapse within 6 years of diagnosis ('poor outcome'). An initial set of cases was analysed for a range of putative prognostic markers and a prognostic index, distinguishing the two outcome categories, was calculated. This index was then validated by testing its predictive power on a second, independent set of cases. A combination of histological grade plus immunochemical staining for BCL-2, p27 and Cyclin D1, generated a useful prognostic index for tamoxifen-treated patients but not for those treated by surgery alone. The value of the index was confirmed in a second set of tamoxifen-treated, early stage breast cancers. Overall, it correctly predicted good and poor outcome in 79 and 74% of cases, respectively (odds ratio 11.0). Other markers assessed added little to prediction of outcome. In the case of molecular assays, sensitivity and reliability were compromised by the age of the tissue specimens and the variability of fixation protocols. In selecting patients for adjuvant systemic chemotherapy, the proposed index improves considerably on current international guidelines and matches the performance reported for 'gene-expression signature' analysis.
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Affiliation(s)
- M McCallum
- Department of Pathology, Victoria Infirmary, South Glasgow University Hospitals NHS Trust, Glasgow, Scotland
| | - C Baker
- Department of Pathology, Victoria Infirmary, South Glasgow University Hospitals NHS Trust, Glasgow, Scotland
- Bute Medical School, University of St Andrews, Scotland
| | - K Gillespie
- Bute Medical School, University of St Andrews, Scotland
| | - B Cohen
- Bute Medical School, University of St Andrews, Scotland
| | - H Stewart
- Scottish Cancer Trials Office, Edinburgh, Scotland
| | - R Leonard
- Department of Clinical Oncology, Lothian University Hospitals NHS Trust, Edinburgh, Scotland
| | - D Cameron
- Department of Clinical Oncology, Lothian University Hospitals NHS Trust, Edinburgh, Scotland
| | - R Leake
- Institute of Biomedical and Life Sciences, University of Glasgow, Scotland
| | - J Paxton
- Department of Pathology, Victoria Infirmary, South Glasgow University Hospitals NHS Trust, Glasgow, Scotland
| | - A Robertson
- Department of Pathology, Ninewells Hospital and Medical School, Dundee, Scotland
| | - C Purdie
- Department of Pathology, Ninewells Hospital and Medical School, Dundee, Scotland
| | - A Gould
- Cancer Intelligence Unit, Common Services Agency of the NHS (Scotland), Trinity Park House, Edinburgh, Scotland
| | - M Steel
- Bute Medical School, University of St Andrews, Scotland
- Bute Medical School, University of St Andrews, Fife KY16 9TS, Scotland, UK. E-mail:
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