THE BUILDING OF A REFERENCE DATABASE OF HUMAN MITOCHONDRIAL DNA NUCLEOTIDE VARIANTS

• Main Author: Restu Prihadi (NIM: 205 05 016), Anton
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/5761
• Institution: Institut Teknologi Bandung

Abstract: <br /> <br /> <br /> <br /> <br /> High degree on human mitochondrial DNA (mtDNA) mutation has become a basic line to make a standard database as a reference to study the variation of normal mutation and also those which cause human disease. Previous research on 1991 using 13 samples revealed 128 nucleotide variants on coding region of mtDNA compare to standard sequence of human mtDNA, Cambridge Reference Sequence (CRS). Until June 2007 there were 2803 complete sequence of human mtDNA on the GenBank database. The aim of this research is to make a more complete database of human mtDNA nucleotide variants using more data than previous research. The first step of this research is collecting the whole complete sequence of human mtDNA from GenBank. All of data collected and then separated to be individual mtDNA data using EditSeq DNASTAR software. Each data then renamed with the access code in the GeneBank database. All of the mtDNA samples were compared to standard sequence of human mtDNA using Human mtDNA Analyzer (H-Man) version 1.2 software to obtain their nucleotide variants. The result of analysis then being transfered to coma delimited (.csv) format and the SeqMan DNASTAR software was used to proof the appropriateness of the H-Man v.1.2 result. All of the nucleotide variants information in every sample became the source of human mtDNA nucleotide variants database. Nucleotide variants data were transferred to a database using spreadsheet macro programs of Microsoft Excel 2003. The next step is constructing a matrix to find every nucleotide variations from every sample that used in this research. After all of the nucleotide variations found, then another database which aligned each sample of human mtDNA to CRS was build, and the sample being clustered according to its base pair length. The analyze steps consist of determination the quantity of human mtDNA nucleotide variants, nucleotide variants distribution, mutation in human mtDNA function and location, also mutation which related to human disease. This research used 2339 from total 2803 data of human mtDNA collected from GenBank database because some of the samples are not full length human mtDNA sequence. According to human mtDNA nucleotide variants database, we found 3998 position of mutation compare to CRS. The total of nucleotide variants in each sample around one percent of 16.5 kb and generally the mutation in human mtDNA randomly distributed. In addition there are 13 position nucleotidevariants which found almost in every sample of human mtDNA. Region of mtDNA which possessed the highest mutation is non coding region, D-Loop. Almost half of this region carried nucleotide variants in 2339 samples that we used in this research. Meanwhile the lowest mutation happened at tRNA coding regions. The result of nucleotide variants which connected to human disease analysis showed some individual diagnosed with specific genetic disease. The consensus sequence for human mtDNA was derived from 2339 samples of human mtDNA. The consensus sequence was constructed from the most commonly observed nucleotides at any particular position in human mitochondrial genome. The consensus sequence differs at 13 nucelotide positions from CRS sequence. Five of these sequences were found in earlier studies using 13 samples of human mtDNA, and this research found another five of human mtDNA consensus sequence. Human mtDNA nucleotide variants database also has benefit as a standard reference to diagnose genetic disease. The establishment of a reference database of nucleotide variants of human mtDNA could facilitated the future study of human mtDNA.