Structural variation in the alleles of a short tandem repeat system at the human alpha fibrinogen locus

Abstract

This paper reports the sequences of 22 alleles identified at the HumFGA (human alpha fibrinogen) short tandem repeat locus in the British Caucasian and Afro-Caribbean populations. Alleles at the lower end of the observed size range were found to increase in size by 4-bp increments with the repeat unit following the pattern TC(TCTT)n. However, 5 alleles were identified that differed in size by 2 bp from the 4 bp increment as a result of the deletion of a TC dinucleotide, or the addition of a TT dinucleotide, immediately prior to the 1st repeat unit. Alleles at the upper end of the observed size range were found to have a more complex repeat unit structure and also exhibited duplication of both 5' and 3' flanking sequences. A nomenclature for the designation of HumFGA alleles is proposed on the basis of this sequence data.

Microsatellite structures in the context of human evolution

“…Especially long variants are found in the Ovambo (Ova) population. The FGA repeat region contains the most variable repeat alteration, which may not only have been caused by base substitutions (T to C and C to T) but also by gene conversion like events for the longer alleles > 27 repeats [21,29]. As with D21S11, longer variants are only observed in Ovambos.…”

Five cases of forensic short tandem repeat DNA typing

“…Due to their structural similarity, simultaneous amplification of the loci (multiplex PCR) followed by semiautomatic detection on a sequencer is possible and allows individualization of most materials within a single day. In contrast to STR systems with a lower discriminating power, complex STR systems like HUM-SE33, HUMFIBRA and HUMD2lSll [8,[51][52][53] with many alleles have a higher information content and thus might be the type of DNA polymorphisms which will mainly be used in the future. However, because of their high number of alleles, those systems need to be electrophoretically resolved down to one base pair each.…”

Sequence analysis and allelic designation of the two short tandem repeat loci D18S51 and D8S1179

“…Sequence analysis of individual D8S 1179 and D 18S51 alleles, isolated from donated blood samples, was carried out as described previously (Barber et al 1995(Barber et al , 1996. However, the following modifications were made: the 1st and 2nd round PCR amplification conditions were 95°C for 60 s, 60°C for 60 s, 72°C for 60 s and a final extension at 72°C for 10 min.…”

“…Solid phase sequencing of the sense and anti-sense strands of D8S 1179 alleles and the antisense (TCTT) strand of D18S51 alleles was carried out using a Prism T7 Sequenase dye terminator single stranded sequencing kit (Applied Biosystems) as described previously (Barber et al 1995(Barber et al , 1996. The sequencing primer was the non-biotinylated primer used in the second round PCR amplification reaction.…”