The Genotyping by the Nucleotide, Length, and Quantitative Polymorphism of C-stretch of HVR I of mtDNA D-Loop

Kim, Ji Young; Jin, Kang Nam; Kim, Hyung Seok; Park, Jong Tae

Abstract

To analyze the nucleotide polymorphism and length polymorphism of C-stretch of HVR 1 (Hypervariable Region I) of mtDNA D-loop in the maternal lineages in Koreans, sequencing of C-stretch, GeneScan analysis and cloning of a cases were performed in 266 random objects and 128 families which were confirmed by STR analysis of autosome, X chromosome and nucleotide polymorphism of mitochondrial DNA D-loop. C- stretch was classified into two groups. First group (the group of nucleotide polymorphism 74.2%) has 14 bases which show nucleotide polymorphism composed of adenine, cytosine and thymine without length polymorphism and second group (poly C tract 25.8%) shows length polymorphism by the changes of the number of adenine and cytosine. The patterns of nucleotide polymorphism were as follows: A4C5TC4 (64.8%), A4C5TC2TC (0.8%), A4C4TTC2TC (0.8%), A4C3TCTC4 (5.5%), A4C2TC2TC4 (0.8%), A4CTC3TC4 (0.8%), A4TC4TC4 (0.8%). The pattern of length polymorphism of poly C tract were as follows : LP10-16 (3.0%), LP11-16 (6.1%), LP11-17 (27.2%), LP11-18 (6.1%), LP12-16 (12.1%), LP12- 17 (39.4%), LP12-18 (3.0%), LP13-16 (3.0%) The copy number ratios of each fragment length in the same pattern of length polymorphism were various, and this data were valuable in individual identification because of the quantitative polymorphism of each fragment length. The correlation coefficients of copy number ratio of each fragment length in the families were more than 0.98 in 84.8% (28 of 33 families) of cases, which was interpreted as maternal inheritance of the copy number ratio of fragment length. However, in some cases (9.1%, 3 of 33 families), the correlation value of fragment length were less than 0.96 and in 2 cases of 33 families (6.1%), were 0.89 and 0.75 which suggested a possibility of mutation in the quantitative polymorphism although the length polymorphism were maternally inherited. From the above results, sequencing analysis of nucleotide polymorphism and GeneScan analysis of C- stretch must be combined to clearly identify the nucleotide polymorphism, length polymorphism, and quantitative polymorphism of C-stretch of HVR 1 of mtDNA D-loop.