Mitochondrial DNA D-loop hypervariable regions: Czech population data

Abstract

In order to identify polymorphic sites and to find out their frequencies and the frequency of haplotypes, the complete D-loop of mitochondrial DNA (mtDNA) from 93 unrelated Czech Caucasians was sequenced. Sequence comparison showed that 85 haplotypes were found and of these 78 were unique, 6 were observed twice and 1 was observed three times. Genetic diversity (GD) was estimated at 0.999 and the probability of two randomly selected sequences matching (random match probability, RMP) at 1.2%. Additionally these calculations were carried out for hypervariable regions 1, 2 (HV1, HV2), for the area between HV1 and HV2 and for the area of the hypervariable region HV3. The average number of nucleotide differences (ANND) was established to be 10.2 for the complete D-loop. The majority of sequence variations were substitutions, particularly transitions. Deletions were found only in the region where HV3 is situated and insertions in the same place and in poly-C tracts between positions 303 and 315 in HV2. A high degree of length heteroplasmy was found especially in the regions of poly-C tracts between positions 16184 and 16193 in HV1 and between positions 303 and 315 in HV2. Position heteroplasmies were found in two cases.

Mitochondrial DNA Variability in Slovaks, with Application to the Roma Origin

“…This and a similar haplotype, lacking only the 16271 transition, are very rare in European Roma populations, being found only in the Spanish, Bulgarian and Hungarian Roma Egyed et al 2007). Among Europeans, such haplotypes have been revealed only in French (0.5%; Dubut et al 2004), Hungarian (0.5%; Egyed et al 2007) and Czech (about 3%; Vanecek et al 2004;Malyarchuk et al 2006b) populations. In the present study, we have found that 2.9% of individuals from eastern Slovakia are characterized by exactly the same J1 * -haplotype.…”

“…All available published data on HVS I mtDNA variability or RFLPs in Slavonic-speaking populations were used for comparative purposes: Bulgarians (Calafell et al 1996;Richards et al 2000), Russians (Malyarchuk et al 1995;Orekhov et al 1999;Richards et al 2000;Malyarchuk et al 2002;Belyaeva et al 2003;Malyarchuk et al 2004); Ukrainians (Malyarchuk & Derenko, 2001), Belorussians (Belyaeva et al 2003), Poles (Richards et al 2000;Malyarchuk et al 2002), Czechs (Richards et al 2000;Vanecek et al 2004;Malyarchuk et al 2006b), Bosnians (Malyarchuk et al 2003;Cvjetan et al 2004), Slovenians (Malyarchuk et al 2003;Zupanic Pajnic et al 2004), Croatians (Tolk et al 2000;Cvjetan et al 2004), Serbians, Herzegovinians and Macedonians (Cvjetan et al 2004).…”

Mitochondrial DNA mutations in human tumor cells

“…Therefore, the high mutational frequency in the D-loop region may not lead to the specific changes in tumors. The D-loop is the site that the mtDNA is nearest to the mitochondrial inner membrane and thus is most susceptible to the damage of ROS (24)(25)(26).…”

Phantom mutation hotspots in human mitochondrial DNA

“…Position 527 is, for example, suspicious in the Czech population data from [72]: sample no. 64 is recorded with a deletion at this position, which seems to be implausiblealthough understandable, given the signals one typically observes at this position.…”