Evaluating length heteroplasmy in the human mitochondrial DNA control region

Abstract

We present allelic data for three known and one new C-tract in the human mitochondrial DNA (mtDNA) control region, and we measure intergenerational mutation rates at such C-tracts. In detail, in a sample of 1,172 mtDNA sequences, we demonstrate the existence of an instability threshold of eight consecutive cytosines, at and above which the phenomenon of length heteroplasmy arises. To determine mutation rates, we draw on mtDNA sequences in up to four generations of 248 pedigrees for families living in high or low-radiation environmental conditions. The high-radiation sample gives the most conservative (fastest) mutation rate likely to be encountered in any forensic context. We find that the C-tract mutation rate is up to 6% per generation, and we observe an excess of cytosine gains over losses. Case studies and guidelines for evaluating mtDNA heteroplasmy are provided.

The link between mitochondrial DNA hypervariable segment I heteroplasmy and ageing among genetically unrelated Latvians

“…In addition, length heteroplasmy found in this region of the HVS-I reproduced a complex DGGE pattern. In our study, individuals with HVS-I motif 126-163-186-189-294 (haplogroup T1) resulting in a string of seven cytosines did not exhibit length heteroplasmy, thereby supporting the hypothesis that eight cytosines is likely the critical number (Melton 2004;Chen et al, 2009;Irwin et al, 2009;Forster et al, 2010).…”

“…Among the studied age groups the 16189C variant was found in two predominate mtDNA phylogenetic branches, haplogroup H and subhaplogroups U (U4, U5 and some minor subgroups of U), which encompass almost 70% of all mitochondrial genomes in the Latvian population (Pliss et al, 2006). Similarly, Forster et al, (2010) showed that a high proportion of 16189C alleles among 1172 mtDNA analyzed sequences were associated with the mtDNA type U1a. The T to C substitution at nucleotide position 16189 leads to C-stretch length heteroplasmy approximately ranging from nps 16184 to 16193 (Bendal and Sykes, 1995;Forster et al, 2010).…”

“…Similarly, Forster et al, (2010) showed that a high proportion of 16189C alleles among 1172 mtDNA analyzed sequences were associated with the mtDNA type U1a. The T to C substitution at nucleotide position 16189 leads to C-stretch length heteroplasmy approximately ranging from nps 16184 to 16193 (Bendal and Sykes, 1995;Forster et al, 2010). In addition, length heteroplasmy found in this region of the HVS-I reproduced a complex DGGE pattern.…”

“…Point (sequence or site) heteroplasmy is defined by sequences presenting different bases at the same nucleotide position, which are usually observed in a sequence electropherogram as a superimposition of two different bases at this nucleotide position (Lutz-Bonengel et al, 2008). Length heteroplasmy is identified by repetitive tracts of consecutive cytosines, and has been found in four regions within the mtDNA control region (Bendall and Sykes, 1995;Lee HY et al, 2004;Forster et al, 2010). However, the observation of heteroplasmy in routine sequencing studies is the exception rather than the rule.…”

Publication of population data of linearly inherited DNA markers in the International Journal of Legal Medicine

“…This is most importantly true for samples exhibiting length heteroplasmy, which require additional sequencing in order to achieve confirmed base call assignment. In particular, we recommend sequencing length heteroplasmic regions with additional primers to unambiguously define the dominant variant, as suggested in [2,5] and references therein.…”