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Reprever: resolving low-copy duplicated sequences using template driven assembly.

Genomic sequence duplication is an important mechanism for genome evolution, often resulting in large sequence variations with implications for disease progression. Although paired-end sequencing technologies are commonly used for structural variation discovery, the discovery of novel duplicated sequences remains an unmet challenge. We analyze duplicons starting from identified high-copy number variants. Given paired-end mapped reads, and a candidate high-copy region, our tool, Reprever, identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon. Reprever resolves ambiguous mapping signatures from existing homologs, repetitive elements and sequencing errors to identify breakpoint. At each breakpoint, Reprever reconstructs the inserted sequence using profile hidden Markov model (PHMM)-based guided assembly. In a test on 1000 artificial genomes with simulated duplication, Reprever could identify novel duplicates up to 97% of genomes within 3 bp positional and 1% sequence errors. Validation on 680 fosmid sequences identified and reconstructed eight duplicated sequences with high accuracy. We applied Reprever to reanalyzing a re-sequenced data set from the African individual NA18507 to identify >800 novel duplicates, including insertions in genes and insertions with additional variation. polymerase chain reaction followed by capillary sequencing validated both the insertion locations of the strongest predictions and their predicted sequence.

Pubmed ID: 23658221


  • Kim S
  • Medvedev P
  • Paton TA
  • Bafna V


Nucleic acids research

Publication Data

July 1, 2013

Associated Grants

  • Agency: NICHD NIH HHS, Id: 1P01HD070494-01
  • Agency: NHGRI NIH HHS, Id: 5R01-HG004962
  • Agency: NHLBI NIH HHS, Id: U54 HL108460
  • Agency: NHLBI NIH HHS, Id: U54-HL108460

Mesh Terms

  • Algorithms
  • DNA Copy Number Variations
  • Genome, Human
  • Humans
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA
  • Software
  • Templates, Genetic