(A) Adapter synthesis. A double-stranded, randomized Duplex Tag sequence is appended to a sequencing adapter by copying a degenerate sequence in one strand of the adapter with DNA polymerase. Complete adapter A-tailing is ensured by extended incubation with polymerase and dATP.
(B) Duplex Sequencing workflow. Sheared, T-tailed double-stranded DNA is ligated to A-tailed adapters. Because every adapter contains a Duplex Tag on each end, every DNA fragment becomes labeled with two distinct tag sequences (arbitrarily designated α and β in the single fragment shown). PCR amplification with primers containing Illumina flow-cell–compatible tails is carried out to generate families of PCR duplicates. Two types of PCR products are produced from each DNA fragment. Those derived from one strand will have the α tag sequence adjacent to flow cell sequence 1 and the β tag sequence adjacent to flow cell sequence 2. PCR products originating from the complementary strand are labeled reciprocally.
(C) Error correction. (i–iii) Sequence reads sharing a unique set of tags are grouped into paired families with members having strand identifiers in either the αβ or βα orientation. Each family pair reflects the amplification of one double-stranded DNA fragment. (i) Mutations (colored spots) present in only one or a few family members represent sequencing mistakes or PCR-introduced errors occurring late in amplification. (ii) Mutations occurring in many or all members of one family in a pair arise from PCR errors during the first round of amplification such as might occur when copying across sites of mutagenic DNA damage. (iii) True mutations (green) present on both strands of a DNA fragment appear in all members of a family pair. Whereas artifactual mutations may co-occur in a family pair with a true mutation, all except those arising during the first round of PCR amplification can be independently identified and discounted when producing (iv) an error-corrected single-strand consensus sequence (SSCS). The sequences obtained from each of the two strands of an individual DNA duplex can then be compared to obtain (v) the duplex consensus sequence (DCS), which eliminates remaining errors that occurred during the first round of PCR.
Detection of ultra-rare mutations by next-generation sequencing
MichaelW. Schmitta, Scott R. Kennedy, Jesse J. Salk, Edward J. Fox, Joseph B. Hiatt,and Lawrence A. Loeb
Michael W. Schmitt, 14508–14513, doi: 10.1073/pnas.1208715109
Next-generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of ∼1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, we have developed a method termed Duplex Sequencing. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors result in mutations in only one strand and can thus be discounted as technical error. We determine that Duplex Sequencing has a theoretical background error rate of less than one artifactual mutation per billion nucleotides sequenced. In addition, we establish that detection of mutations present in only one of the two strands of duplex DNA can be used to identify sites of DNA damage. We apply the method to directly assess the frequency and pattern of random mutations in mitochondrial DNA from human cells.