The paper presents a method called Safe-Sequencing System ("Safe-SeqS") to improve the detection and quantification of rare mutations using massively parallel sequencing. The approach involves assigning unique identifiers (UIDs) to each DNA template molecule, amplifying these uniquely tagged molecules to create UID families, and then redundantly sequencing the amplification products. A mutation is considered a "supermutant" if at least 95% of the UID family members contain the same mutation. This method significantly reduces the false positive rate by ensuring that mutations are only identified if they are consistently present across multiple copies of the same UID. The study demonstrates the utility of Safe-SeqS in determining the fidelity of a polymerase, the accuracy of in vitro synthesized oligonucleotides, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells. The method was tested on various samples, including DNA from normal human cells and mitochondrial DNA, and showed a significant reduction in apparent mutation frequency compared to conventional sequencing methods. The Safe-SeqS approach can be applied using either endogenous or exogenous UIDs. Endogenous UIDs are naturally occurring sequences at the ends of DNA fragments, while exogenous UIDs are artificially introduced through PCR. The method allows for the analysis of a large number of template molecules with high accuracy, even in clinical samples where mutation prevalence is very low. The study also highlights the importance of detecting rare mutations in both basic and clinical research, as these mutations can provide insights into disease progression, drug resistance, and other critical biological processes. The Safe-SeqS method offers a reliable way to identify and quantify rare mutations, improving the accuracy of next-generation sequencing data. The results show that Safe-SeqS can reduce the apparent mutation frequency by up to 24-fold in genomic DNA and 15-fold in mitochondrial DNA. The method is also applicable to various sample types and can be used to assess the reliability of oligonucleotide synthesis and polymerase fidelity. Despite its advantages, the method has limitations, such as the need for multiple amplification cycles and the potential for template loss during the process. However, the study demonstrates that Safe-SeqS is a powerful tool for detecting rare mutations with high accuracy and reliability.The paper presents a method called Safe-Sequencing System ("Safe-SeqS") to improve the detection and quantification of rare mutations using massively parallel sequencing. The approach involves assigning unique identifiers (UIDs) to each DNA template molecule, amplifying these uniquely tagged molecules to create UID families, and then redundantly sequencing the amplification products. A mutation is considered a "supermutant" if at least 95% of the UID family members contain the same mutation. This method significantly reduces the false positive rate by ensuring that mutations are only identified if they are consistently present across multiple copies of the same UID. The study demonstrates the utility of Safe-SeqS in determining the fidelity of a polymerase, the accuracy of in vitro synthesized oligonucleotides, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells. The method was tested on various samples, including DNA from normal human cells and mitochondrial DNA, and showed a significant reduction in apparent mutation frequency compared to conventional sequencing methods. The Safe-SeqS approach can be applied using either endogenous or exogenous UIDs. Endogenous UIDs are naturally occurring sequences at the ends of DNA fragments, while exogenous UIDs are artificially introduced through PCR. The method allows for the analysis of a large number of template molecules with high accuracy, even in clinical samples where mutation prevalence is very low. The study also highlights the importance of detecting rare mutations in both basic and clinical research, as these mutations can provide insights into disease progression, drug resistance, and other critical biological processes. The Safe-SeqS method offers a reliable way to identify and quantify rare mutations, improving the accuracy of next-generation sequencing data. The results show that Safe-SeqS can reduce the apparent mutation frequency by up to 24-fold in genomic DNA and 15-fold in mitochondrial DNA. The method is also applicable to various sample types and can be used to assess the reliability of oligonucleotide synthesis and polymerase fidelity. Despite its advantages, the method has limitations, such as the need for multiple amplification cycles and the potential for template loss during the process. However, the study demonstrates that Safe-SeqS is a powerful tool for detecting rare mutations with high accuracy and reliability.