External contamination in single cell mtDNA analysis

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• Mitochondrial DNA (mtDNA) variation is studied in various cell types and tissues, including challenging samples like single cells and degraded specimens.
• External DNA contamination is a persistent challenge, potentially compromising the integrity and accuracy of mtDNA research.

Purpose of the Study:

• To investigate the origins of anomalous mitochondrial DNA (mtDNA) sequence patterns observed in single hematopoietic cells.
• To assess the effectiveness of current methods in identifying and eliminating external DNA contamination in mtDNA studies.

Main Methods:

• A phylogenetic approach was employed to analyze the geographic origins of mtDNA sequence anomalies.
• 7094 single hematopoietic cells were analyzed for variations in mtDNA sequence.

Main Results:

• Forty events with irregular mtDNA patterns were detected, with eight traced to laboratory personnel and six to sample cross-contamination.
• The remaining anomalous mtDNA sequences, potentially from East Asia, Africa, or West Eurasia, were attributed to contamination.
• An estimated 0.6% external contamination rate was observed, emphasizing the issue's significance.

Conclusions:

• Geographic origin determination of anomalous mtDNA types aids in identifying contamination sources.
• Routine analysis of laboratory personnel is insufficient to detect all contaminants.
• Improved quality control measures, including phylogenetic analysis, are crucial for accurate single-cell mtDNA research and preventing misdiagnosis of diseases like cancer.