Allelic Ladder Characterization of the Short Tandem Repeat Polymorphism in Intron 6 of the Lipoprotein Lipase Gene and Its Application in an Austrian Caucasian Population Study

Glock, B.; Schwartz, D. W. M.; Schwartz-Jungl, E.M.; Mayr, Wolfgang R.

doi:10.1520/jfs13958j

Cited by 9 publications

(7 citation statements)

References 21 publications

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“…D12S391 D12S391 has been described as a compound STR locus consisting of two different repeat motifs (AGAT) and (AGAC). Most of the alleles follow the regular repeat structure (AGAT) [8][9][10][11][12][13][14][15][16][17] (AGAC) 6-10 [4]. Some alleles (220 bp, 224 bp) show an incomplete repeat (GAT) at the second position of the repeat array [8].…”

Section: Humvwamentioning

confidence: 99%

Further sequence and length variation at the STR loci HumFES/FPS, HumVWA, HumFGA and D12S391

et al. 2000

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This paper reports population data and statistics for the HumFES/FPS, HumVWA, HumFGA and D12S391 loci in Austria. The sequences of some rare and new variant alleles which have been identified in the course of the present population study and other investigations are described. Sequence variation occurred in a HumFES/FPS allele revealing an (ATTT)9 structure and an A to C transversion in the 5' flanking region. At the HumVWA locus the structural type of the common allele 14 has been found in one allele 13 and in three examples of allele 15. Additionally the TCTA (TCTG)3(TCTA)n structure has been observed in three examples of allele 13 and one allele 14, which is very uncommon. Another allele 14 showed a C to T transition in the third of nine TCTA repeats. The sequences of three length variations at the HumFGA locus, namely the alleles 16, 19.2 and 21.2 are reported. At the D12S391 locus a novel 19.1 allele was found in this study. An extended nomenclature is proposed for the HumVWA locus to denominate sequence variants in a precise but simple way.

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Section: Humvwamentioning

confidence: 99%

Further sequence and length variation at the STR loci HumFES/FPS, HumVWA, HumFGA and D12S391

et al. 2000

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“…Strand separation and single stranded sequencing (solid phase) was conducted on an A.L.F. automatic sequencer (Pharmacia, Sweden) as previously described [8].…”

Section: Sequencingmentioning

confidence: 99%

“…In the repeat regions of all alleles an isolated T was observed after 10-17 repeats and an ATCCT unit was observed after a single ATCT repeat. A basic sequence structure of (ATCA) 1-3 (ATCT) 2,10-13 (ATC) 0-1 (ATCT) 0,5,9-12 T (ATCT) ATCCT (ATCT) 2,[8][9][10][11]13 (ACCT) 0-1 (ATCT) 0.8-11 was found. Figure 2 shows a typical electropherogramm of the D17S976 system on a horizontal, native PAGE while Fig.…”

Section: Sequence Structure Of D17s976 Allelesmentioning

confidence: 99%

Genetic variation and sequence studies of a highly variable short tandem repeat at the D17S976 locus

Klintschar

Glock

Dauber

et al. 1998

International Journal of Legal Medicine

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The STR locus D17S976 was investigated by PCR amplification and native polyacrylamide gel electrophoresis in 158 unrelated Austrian Caucasians. No deviations from Hardy-Weinberg expectations were observed. The mean exclusion chance was 0.792, the discriminating power was 0.980 and the observed heterozygosity rate was 0.873. Moreover two alternative denaturing electrophoretic protocols are proposed. An allelic ladder consisting of 14 sequenced alleles (236-288 bp) was constructed. Sequence analysis revealed that the locus contained three different repeat motifs: ATCA, ATCT and ACCT, all of which vary in number between alleles. The aggregate number of the three tetrameric repeat types was used for allele designation. As a repeat with a single base deletion (ATC) was found in both the smallest and the largest alleles, a ".3" was added to the allele designation in those cases. Therefore the smallest allele is designated 19.3, and the largest allele is designated 32.3. To evaluate the exact extent of sequence variation more extensive sequence studies are necessary.

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“…There are many reports on the frequency of the STR polymorphisms located at intron 6 of the lipoprotein lipase (LPL) locus [1][2][3][4][5][6][7][8][9][10][11][14][15][16][17][18] . Because the allelic sizes of this locus are comparatively small (111-135 bp), it is considered to be suitable for the detection of polymorphisms from highly degraded DNA.…”

Section: Introductionmentioning

confidence: 99%

Polymorphism of LPL Locus in Japanese and Comparison of PCR Amplification Efficiency from Degraded DNA between LPL Locus and the D21S11

Maruyama

Minaguchi

2005

Bull. Tokyo Dent. Coll.

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The short tandem repeat (STR) polymorphism of the lipoprotein lipase (LPL) locus was amplified by PCR and analyzed using denaturing polyacrylamide gel electrophoresis followed by silver staining. Among 158 DNA samples from the Japanese population, six alleles were observed. When the sequences of the allelic products were compared, each allelic segment contained 7 and 9-13 TTTA tetranucleotide repeat motifs. Genotypic distribution met Hardy-Weinberg expectations, and included heterozygosity was 48.8%. Most of the Japanese genotypes allele 10. When PCR amplification efficiency for the LPL locus from degraded DNA was compared with that for the D21S11 locus in terms of amplification size, increase in amplification size showed a considerable influence on amplification efficiency, producing inaccurate amplification, such as unbalanced amplification, or amplification of non-target PCR products. These results suggest that reduction in amplification size increases the accuracy and efficiency of PCR amplification from highly degraded DNA.

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Allelic Ladder Characterization of the Short Tandem Repeat Polymorphism in Intron 6 of the Lipoprotein Lipase Gene and Its Application in an Austrian Caucasian Population Study

Cited by 9 publications

References 21 publications

Further sequence and length variation at the STR loci HumFES/FPS, HumVWA, HumFGA and D12S391

Further sequence and length variation at the STR loci HumFES/FPS, HumVWA, HumFGA and D12S391

Genetic variation and sequence studies of a highly variable short tandem repeat at the D17S976 locus

Polymorphism of LPL Locus in Japanese and Comparison of PCR Amplification Efficiency from Degraded DNA between LPL Locus and the D21S11

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