Mitochondria analysis

Sequencing quality comparison based on MtDNA

The rCRS genome has  accepted as a refercence genome for mitochondria.

We compaired the rCRS genome with KoRef mtDNA.

As the Table1, the two genomes has showed very similar in sequence composition.

Sequences of genes were aligned very clear (not appear stop codons). (figure 1)

Table 1. Comparison rCRS with KoRef mtDNA in sequence composition.

Variation aspect of mitochondrial genome

13 mitochondrial protein coding genes, 12 rRNA genes, and  22 tRNA genes were identified by aligning with the rCRS mitochondrial genome sequences using Clustal W.

Figure 1. Annotation and visualization of KoRef mitochondria genome. Variations and genes of the genome were identified through sequence alignment against rCRS.

Table 2.  Genes involved in KoRef mitochondria genome.

Table 3. Nucleotide substitutions in KoRef mtDNA against rCRS genome. 

MtDNA ethno-genographic lineage

Fig XX. mtDNA ethno-genogeographic lineage

Korean mitochondrial DNA had on XX SNPs. According to 22 haplogroups defined by sequence differences from the rCRS, haplogroup D4, prevalent in Asia, mapping into our mtDNA.

Mapping disease information

We have been able to detect the expected phenotype based on the literature given the according to published literature (ref 1)

Position: A1438G

Disease:    Diabetes Mellitus

Heteroplasmy

possibility

• paternal inheritance (ref 2)
• by aging, MtDNA variation in one indivisual is increasing.

Observed heteroplasmy

 10 =< MHP < 50% : 6

5 <= MHP < 10 : 16

1 <= MHP < 5 : 1188 

MHP: Minor-heteroplasmy

Table 4. Heteroplasmic mtDNA changes in KoRef mtDNA.

References

1. Tawata, M., Ohtaka, M., Iwase, E., Ikegishi, Y., Aida, K. and Onaya, T. (1998). "New mitochondrial DNA homoplasmic mutations associated with Japanese patients with type 2 diabetes." Diabetes 47(2):276-277.    9519725

2. Gustafson A. W., Heckerling P. S., Vissing J., Schwartz M. (2002). Paternal Inheritance of Mitochondrial DNA. N Engl J Med 347: 2081-2082