C2_4_4 microheterogeneity and HLA Class I.

The microheterogeneity of the tetranucleotide repeat locus C2_4_4 situated in the HLA class I region (6p21.3) was investigated by sequencing 50 alleles in an Austrian population sample of 240 unrelated Caucasoid individuals. Several different sequences were found in alleles of the same length. Analysis of the associations between the sequenced C2_4_4 alleles and HLA class I showed a strong linkage disequilibrium between the C2_4_4*9 sequence variants and two different HLA class I haplotypes, as well as between the most common *17 sequence and one HLA-ABC haplotype. No clear cut association could be observed in C2_4_4*16 and *18. The results of this study demonstrate that the exclusive use of microsatellite polymorphisms for the definition of HLA haplotypes is generally not possible.

DNA profiling: a valuable tool for quality control of sample logistics including occurrences of suspected sample confusion in a blood donation centre.

BACKGROUND AND OBJECTIVES: A molecular method for analysing whole-blood samples should be established for quality control of plasma sample logistics. MATERIALS AND METHODS: DNA profiles of retention samples (plasma) were compared to profiles of recent donations (whole blood). DNA extraction, amplification and detection were performed using the Qiagen DNA Blood Mini kit, the AmpFFISTR Profiler Plus Kit and capillary electrophoresis, respectively. RESULTS: Matched pairs of full profiles were obtained for all samples investigated, therefore no deviation from the standardized procedures was detected. CONCLUSIONS: Modified extraction and amplification protocols enabled DNA profiling to be used for the quality control of plasma samples. Hence, DNA profiling can be used in the blood bank as a safe and easy method for quality control of sample logistics.

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

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.

A dispermic chimerism in a 2-year-old Caucasian boy.

Detection of two different cell populations in a child is a rare event. The following case of a dispermic chimera was diagnosed before surgery due to problems in blood group determination. A 2-year-old phenotypically male child was admitted for correction of a penoscrotal hypospadia and unilateral cryptorchism. During presurgical laboratory investigation, difficulties in blood group determination occurred. Blood group typing was performed by the DiaMed-ID Micro Typing System and by FACS. Additionally, cytogenetic analysis of lymphocytes and analysis of DNA polymorphisms in different tissues were performed. Two populations of red blood cells were detected, O cells accounting for 75% and B cells for 25%. Analysis of DNA-PCR polymorphisms in lymphocytes, nails, and in cells of the oral mucous membrane demonstrated a chimerism, with two alleles inherited from the father and one from the mother. A cytogenetic analysis of cultured lymphocytes showed a mosaic 46, XY/46,XX. Surgery revealed a prostatic utricle grade III, also called pseudovagina; genitography confirmed a vagina. Bilateral gonad biopsy showed a testis on one side and an ovary on the other. This case of chimerism represents a true hermaphroditism that most probably developed by double fertilization of one or more egg nuclei by two sperms.

A case of dispermic chimerism: importance of DNA polymorphisms.

A case of dispermic chimerism is presented. The use of DNA polymorphisms in order to differentiate between blood chimerism and dispermy is shown.

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

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.

Population study of the STRs HUMCD4 and HUMF13A1 in Catalonia (Northeast Spain).

Allele and genotype frequencies were determined in a population sample from Catalonia (northeast Spain) for two short tandem repeat loci (HUMCD4 and HUMF13A1), using the polymerase chain reaction (PCR). After denaturing PAG electrophoresis, 6 alleles were identified for HUMCD4 in a sample of 157 unrelated individuals, and 11 alleles for HUMF13A1 in a sample of 141 individuals. No deviation from Hardy-Weinberg equilibrium was found. The HUMCD4 and HUMF13A1 loci demonstrated a heterozygosity of 0.6815 and 0.7305 respectively.

A new allele at the short tandem repeat locus HumF13A01.

We investigated the (AAAG)n short tandem repeat (STR) polymorphism HumF13A01 an Austrian Caucasoid population sample (n = 674). PCR amplified fragments were detected on an automatic A.L.F. DNA sequencer using laser-induced fluorescence. A total of 14 alleles could be identified including a new 179 bp allele which was designated allele 3. Sequence determination of allele 3 confirmed the typing results by revealing three continuous copies of the core repeat, whereas in sequencing of 54 additional alleles no further variants or microheterogeneities could be observed. The population data showed no significant deviation from Hardy-Weinberg equilibrium.

Additional variability at the D12S391 STR locus in an Austrian population sample: sequencing data and allele distribution.

The highly polymorphic STR locus D12S391 was investigated in an Austrian population sample (N = 150) by PCR-amplification, comparative detection on native and denaturing polyacrylamide gels and solid phase single stranded sequencing of three size variant alleles and several additional alleles. A total of 15 alleles, distinguishable by size under denaturing conditions, could be detected. No deviations from Hardy-Weinberg equilibrium were observed in the population investigated (P = 0.52). Sequencing of size variants designated 17.3 and 18.3 showed an incomplete (GAT) repeat unit at position two of the tandem region. Additional new sequence variants due to varying compositions of the number of (AGAT) and (AGAC) repeats could be identified. Due to distinct electrophoretical mobilities of alleles of the same size but different sequence structures, denaturing detection conditions should be employed when the aim is standardization.

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.

The short tandem repeat (STR) polymorphism HumLPL (TTTA)n, which is located in intron 6 of the lipoprotein lipase gene, was investigated by AMPFLP (amplification fragment length polymorphism)-technique using an allelic ladder consisting of amplified alleles of this locus as a standard size marker. The allelic ladder was prepared by pooling equal concentrations of six separate alleles, which were identified by their different electrophoretic mobility in native polyacrylamide gel, eluted and subsequently amplified. Sequence analysis of the ladder alleles and allele 7, which is not included in the ladder, showed a regular repeat structure with 7 and 9 to 14 repetitions of the core repeat. The allelic ladder was employed in the analysis of the genotypes of 550 unrelated Caucasoids of Austria. No new alleles were found. The population investigated showed no deviation from Hardy-Weinberg equilibrium (P = 0.195).

Sequence determination of an allele ladder for the STR polymorphism at the CD4 locus and application of the ladder in testing an Austrian Caucasian population sample.

The short tandem repeat (STR) polymorphism at the CD4 locus, designated HUMCD4, was examined by PCR, native polyacrylamide electrophoresis and subsequent silver staining using an allelic ladder of eight distinguishable alleles occurring in an Austrian Caucasian population sample as a standard size marker. The ladder was produced by pooling equal concentrations of eluted, separately amplified and sequenced alleles, which were previously identified by their different electrophoretical migration. Components of the ladder are in regular intervals of five basepairs. Alleles 4 to 8 were designated according to the number of AAAAG repeat units. The four longer alleles 8' to 11 showed a stable A to G transition in one of the repeat units and were designated counting the AAAGG unit for a AAAAG. Allele 8' was not included in the ladder because it showed the same electrophoretic mobility as allele 8. This ladder proved to be a precise and reliable tool in the analysis of 600 chromosomes of the Austrian population. The population investigated showed no deviation from Hardy-Weinberg equilibrium (P = 0.23).