Searching for Appropriate Statistical Parameters for Validation of Mitochondrial DNA Database / 대한법의학회지

Recently, studies on mitochondrial DNA (mtDNA) have increased rapidly. Conventional parameters, such as diversity index, pairwise comparison, are used to interpret and validate data on autosomal DNA; however, the use of these parameters to validate data from mitochondrial DNA databases (mtDNA DBs) needs to be verified because of the different transmission patterns of mtDNA. This study was done to verify the use of these conventional parameters and to test the "coverage concept" for a new parameter. The mtDNA DB is not very big; however, it is necessary to check how the change in parameters corresponds to the DB size. For this, we artificially rearranged a Korean DB into several small sub-DBs of variable sizes. The results show that the diversity in nucleotide variations and the different haplotype numbers do not vary as the size of DB increases. However, the "coverage" changed a lot. The coverage increased from 0.113 in a DB of 100 people to 0.260 in a DB of 653 people. Additionally, using the "coverage concept", we predicted how the total number of haplotypes changed with variations in the sub-DB size and compared the predicted result with final result. In conclusion, "coverage", in addition to conventional statistical parameters, can be used to check the usability of an mtDNA DB. Finally, we tried to predict the size of the whole mtDNA number in Korea using "saturation concept".

Experience on Sequencing of Mitochondrial DNA from 1200 Year Old Bone Using Cloning / 대한법의학회지

Ancient bones have undergone natural decomposition and have been exposed to external environment for long period. Ancient DNA from old bone is usually fragmented. In addition, various kinds of inhibitors are co-extracted. All these may inhibit proper sequencing reaction. Cloning is regarded as the standard method when sequencing aDNA. When cloning, each clone from the same sample may not be of same sequence, and to exact consensus sequence may be difficult. Here we present our experience on 1200 year old bone from Russia, Primorsky Kray area. We have tried to sequence for HV I, II region of mtDNA using modified mini-primer set, which consisted of 7 set to cover the HV I, II. We cloned the PCR product and sequenced all the clones. Amplification efficiency and subsequent success rates were different for each mini primer set. Loci of variation that differ from consensus sequences were rather frequent, and the pattern were variable depending on sample. Except major polymorphic sites that are important when haplogroup designation, 16129 was the most frequent site that was discarded when extracting haplogroup designation.

Unusual mtDNA sequencing results from ancient DNA / 대한법의학회지

Sequence analysis of human mitochondrial DNA(mtDNA) is being used widely to characterize individual identification, particularly when there is insufficient nuclear DNA in samples for typing. Hair shafts, bones, teeth and other samples that are severely decomposed may be subjected to mtDNA analysis. As sample decomposes, however, the possibility of mtDNA to be degraded becomes high and the possibility of spurious results becomes high. In this case mtDNA sequencing results must be carefully analyzed. We got unusual results while typing two human bone samples, which were not compatible with human mtDNA sequence. Bones were about 50 and 35 years old. We report the results with discussions about ancient DNA sequencing.

State of Individual Identification Using Genetic Polymorphism in Korea: Step to Criminal DNA Bank / 대한법의학회지

There have been several attempts for criminal DNA profiling in Korea, but ended without any fruitful results. Recently new movement for the profiling has just been started. Many have to be solved in advance, which can be divided largely into two, technical aspects and legal system which could support the application. To build up profiling for any purpose, work for the standardization must be driven, because many are involved in the work. Authors have checked the status of the DNA typing in Korea and have reviewed its quality by statistical approach. All the popular forensic journals, Korean or international covering from 1997 to 2004, were reviewed to check whether it contains articles on Korean. All the articles containing genetic data on Korean were selected and their results were compared statistically. Total 67 articles were chosen. Articles were on 116 loci, among which 54 were autosomal, 32 were Y chromosomal and the remaining were X chromosomal. Among 32 Y chromosomal loci, 11 were bi-allelic. For the 50 loci two or more lab reported separately. For these loci the results from different lab were compared. There was no statistically significant difference for most of the loci, but some of the loci, especially on Y chromosomal STR loci, showed some differences. Data were showed with some review.

Heteroplasmy Pattern Within D-loop Region of Mitochondrial DNA in Koreans / 대한법의학회지

Mitochondrial DNA (mtDNA) sequencing has been validated as a useful tool in forensics. However, there are several aspects that need to be considered in order for it to be used as firm evidence in a courtroom. Heteroplasmy is one of those. Heteroplasmy means the status that different mtDNA populations exist in a single individual, tissue, cell or even mitochondrion. As the underlying phenomenon of heteroplasmy and polymorphism is similar, care must be taken in analyzing the data from the samples with heteroplasmy. Heteroplasmy can reinforce the use of mtDNA however if we know a lot about it. For this much has to be revealed. In this we screened 494 unrelated Korean using DGGE for the D-loop to determine how frequent heteroplasmy is, and the heteroplasmy pattern was confirmed through sequencing. This paper discussed the results of a comparison with other reports along with several aspects of heteroplasmy.

Bi-allelic loci on Y chromosome in Korean / 대한법의학회지

Recently studies about bi-allelic markers such as SNP, which is commonly found in about every 1.2 kb, seem to be increasing. Compared to STR marker, much have to be improved if it is to be used for individual identification. Nevertheless many researchers have interests in SNP and it 's scope is unpre-dictable. SNP may be promising as an auxiliary tool in individual identification, especially in Y chromo-somal study, in which the usefulness of conventional STR markers are restricted as the concept of haplo-type is applied. We report allelic distribution pattern in Korean for several previously known bi-allelic markers, that are SY81, M9, SRY1532, SRY2627, YAP. In three loci that are SY81, SRY1532, SRY2627, no polymorphism was noted. In M9, YAP loci, bi-allel-ic polymorphism was noted. In M9, 79.3% was G-type, and C-type was 20.7%. The YAP insertion was positive only in 6%. Remaining 94% was YAP(-). These pattern was compared with that of other popu-lation, and racial difference was evident. Several key points about SNP were discussed.

DGGE assay for heteroplasmy in mitochondrial DNA / 대한법의학회지

Heteroplasmy in the hypervariable region 1 of the mtDNA was screened using DGGE. Blood samples from 150 unrelated Koreans were used. Appropriate condition was set up using mixed samples with previously known HV1 sequences. This method is capable of detecting heteroplasmic proportion less than 5 %. Multiple bands pattern meaning heteroplasmy was observed in 41 individuals (27.3%). The majority of heteroplasmic variants could not be detected by direct sequencing of PCR products. For the distribution pattern of heteroplasmy in different tissues within one individual, 14 autopsy cases were screened. Out of these, two were heteroplasmic, but there was no difference between various tissues in the heteroplasmic DGGE band pattern.