Korean J Leg Med.  2014 May;38(2):59-65. 10.7580/kjlm.2014.38.2.59.

Searching for Appropriate Statistical Parameters for Validation of Mitochondrial DNA Database

• Choung CM
• Lee JH
• Cho S
• Lee SD

• KMID: 1849354
• DOI: http://doi.org/10.7580/kjlm.2014.38.2.59

Abstract

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".

Keyword

mtDNA DB; Statistical parameter; Coverage; Phylogeny; Saturation curve

MeSH Terms

DNA
DNA, Mitochondrial*
Haplotypes
Korea
Phylogeny
DNA
DNA, Mitochondrial

Figure

• 

  Fig. 1. Saturation curves of expanded sample sizes. a. Expanded up to 10,000 people b. Expanded up to 100,000 people A result of examining the number of possible observed haplotypes when group size increased up to 10,000, 100,000, the final expected number of haplotypes was 4,500 over. The shaded portion of the graph is the confidence interval upper and lower limits.

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  Fig. 2. Result of simulated saturation curve from N. of observed haplotypes. Graph is obtained by curve expert professional 1.6.5 version. The fit converged to a tolerance of 1e-006 in 5 iterations. No weighting is used.

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