Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA.

ABSTRACT: Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting of reverse complementary sequence at the 5' and 3'-ends of sequencing reads. The palindromic sequences themselves have specific properties - the bases at the 5'-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3'-end. The terminal 3' bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA), which can be ligated and amplified in particular library creation protocols. We propose tha

SUBMITTER: Star B 

PROVIDER: S-EPMC3946424 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature