Comparison of slab gel electrophoresis and capillary electrophoresis for the detection of the fluorescently labeled polymerase chain reaction products of short tandem repeat fragments

Deforce, Dieter; Millecamps, Rebecca; Hoofstat, David Van; Eeckhout, Elfriede G. Van den

doi:10.1016/s0021-9673(97)00394-4

Cited by 35 publications

(25 citation statements)

References 13 publications

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“…The use of dHPLC-based SNP detection was effective in this study, but the analysis was more time consuming than assaying for SSRs because it required the amplification of IR24 DNA as an internal control which needed to be run individually for each recombinant to distinguish between the two homozygous classes. However, several of the technologies available for high through-put SNP and SSR detection, such as oligo nucleotide-based arrays (Cho et al 1999) and multiplexed arrays in capillary machines (Deforce et al 1998), respectively, make rapid screening of large populations very routine using either of these technologies.…”

Section: Discussionmentioning

confidence: 99%

High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.)

et al. 2003

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The xa5 resistance gene from rice provides recessive, race-specific resistance to bacterial blight of rice caused by the pathogen Xanthomonas oryzae pv oryzae. A high-resolution genetic map of the chromosomal region surrounding xa5 was developed by placing 44 DNA markers on the distal end of rice chromosome 5. The basis for mapping was a PCR-based screening of 1,016 F(2) individuals derived from a cross between a near-isogenic line (NIL) and its corresponding recurrent parent to identify recombinants in the region. Recombinant F(2) individuals were progeny tested using F(3) families inoculated with the Philippine strain PXO 61 of bacterial blight pathogen. The xa5 gene was mapped to a 0.5-cM interval between the markers RS7 and RM611, which spanned an interval of approximately 70 kb and contained a total of 11 open reading frames. Sequence data for the locus was generated from an Indica (the IR24 isoline, IRBB21) BAC covering part of the region and compared to other overlapping Indica (cv 93-11) and Japonica (cv Nipponbare) sequences. Candidate-gene analysis revealed that a basal transcription factor (TFIIa), an ABC transporter, a tRNA synthase, a MAP kinase and a cysteine protease, as well as four unknown, hypothetical or putative proteins, are encoded at the locus and could be potential candidates for the resistance gene product. The mechanism by which these genes could provide recessive, race-specific resistance will be elucidated by map-based cloning of the xa5 gene.

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Section: Discussionmentioning

confidence: 99%

High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.)

et al. 2003

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“…This person is a member of the laboratory but did not interfere with any experiments described here. DNA of all samples was extracted using a slightly modified chelex extraction method [13,14]. To obtain more sensitive results for the analysis of three fingerprints to one fingerprint a modified chelex extraction was also used.…”

Section: Sample Treatment and Extractionmentioning

confidence: 99%

DNA typing of fingerprints using capillary electrophoresis: Effect of dactyloscopic powders

et al. 1999

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“…Most of the approximately 400 million short tandem repeat (STR) loci in the human genome show polymorphic alleles that differ in length ( Craig et al 1988;Edwards et al 1991;Deforce et al 1998). These differences in length are caused by the number of repetitions of a 2-6 bp (base pair) sequence.…”

Section: Introductionmentioning

confidence: 99%

A new pentaplex PCR system for forensic casework analysis

Lederer

Seidl²,

Graham³

et al. 2000

International Journal of Legal Medicine

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In 1998 the Federal Criminal Police Office of Germany (BKA) established a central genetic database of offenders and suspects to facilitate comparisons with biological samples from future criminal offences. The five obligatory short tandem repeat (STR) loci in this database (TH01, SE33, vWA, FGA and D21S11) were co-amplified in a new PCR pentaplex analysing system together with the sex-specific locus amelogenin. Due to overlapping fragment sizes, amplification products were fluorescent dye-labelled with different colours, separated by electrophoresis and detected directly using the ABI PRISM 310 Genetic Analyzer. Reproducible and reliable results were obtained from as low as 125 pg template DNA, indicating high specificity and sensitivity of the assay. Environmental studies and enzymatic digest with DNase I revealed an excellent stability of the pentaplex system with typeable results even in cases of partially degraded DNA. Complete and reproducible DNA typing was possible in blood-stain mixtures with the minor component as low as 10%. Mean stutter peak intensities were analysed for all loci and ranged from 2.7 +/- 0.8% (TH01) to 10.6 +/- 1.6% (vWA) of the main signal intensity. Allele frequencies were determined in a North Bavarian population sample (n = 121). The combination of five systems resulted in a mean exclusion chance of 99.86% and a power of discrimination of 99.999996%. No deviation from Hardy-Weinberg equilibrium could be found.

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Comparison of slab gel electrophoresis and capillary electrophoresis for the detection of the fluorescently labeled polymerase chain reaction products of short tandem repeat fragments

Cited by 35 publications

References 13 publications

High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.)

High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.)

DNA typing of fingerprints using capillary electrophoresis: Effect of dactyloscopic powders

A new pentaplex PCR system for forensic casework analysis

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