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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
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Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling.

Chun-Tien Chang1, Chi-Neu Tsai, Chuan Yi Tang

  • 1Department of Computer Science, National Tsing Hua University, Hsin-Chu, Taiwan.

Thescientificworldjournal
|July 11, 2012
PubMed
Summary
This summary is machine-generated.

A new program, Mixed Sequence Reader (MSR), analyzes heterozygous chromatogram data to identify genetic variants like SNPs, indels, STRs, and paralogous genes. This tool aids in diverse applications, from genetic profiling to viral genotyping.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Direct sequencing of PCR products yields heterozygous chromatograms valuable for identifying genetic variations such as single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes.
  • Existing tools like Indelligent and ShiftDetector effectively detect indels and STRs but lack the capability to analyze heterozygous base-calling chromatogram data for other genomic variants.
  • The analysis of heterozygous base-calling fluorescence chromatogram data for diverse genomic variant detection remains a challenge due to the absence of suitable analytical tools.

Purpose of the Study:

  • To develop a free, web-based program named Mixed Sequence Reader (MSR) for the direct analysis of heterozygous base-calling fluorescence chromatogram data.
  • To enable the identification and analysis of various genomic variants by comparing .abi files with reference sequences.
  • To provide a versatile tool for applications including genetic profiling, viral genotyping, and gene copy number estimation.

Main Methods:

  • Developed Mixed Sequence Reader (MSR), a free web-based program for analyzing heterozygous base-calling fluorescence chromatogram data in .abi file format.
  • Implemented a method to identify heterozygous sequences as two distinct sequences and align them with reference sequences.
  • Utilized NCBI reference sequences, the Federal Bureau of Investigation Combined DNA Index System (CODIS), and viral databases for comparative analysis.

Main Results:

  • MSR can physically locate indel and STR sequences and determine STR copy number by referencing NCBI sequences.
  • The program can predict microsatellite patterns using CODIS data.
  • MSR is capable of determining human papilloma virus (HPV) genotypes in cases of co-infections by querying viral databases.
  • The tool can estimate the copy number of paralogous genes, exemplified by DEFB4 and HSPDP3.

Conclusions:

  • Mixed Sequence Reader (MSR) is a novel, free web-based tool designed for analyzing heterozygous base-calling fluorescence chromatogram data.
  • MSR facilitates the identification and characterization of diverse genomic variants, including indels, STRs, and paralogous genes, by comparison with reference sequences.
  • The program offers broad applicability in genetic research, forensic science, and clinical diagnostics, enhancing the analysis of complex genetic information.