a survey of genomic traces reveals a common sequencing error, rna editing, and dna editing基因组的调查揭示了一个共同的痕迹测序错误,rna编辑,编辑和dna.pdfVIP

A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing 1. 1,2. 3 4 1 Alexander Wait Zaranek *, Erez Y. Levanon *, Tomer Zecharia , Tom Clegg , George M. Church 1 Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America, 2 The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel, 3 Compugen Ltd., Tel Aviv, Israel, 4 Scalable Computing Experts, Somerville, Massachusetts, United States of America Abstract While it is widely held that an organism’s genomic information should remain constant, several protein families are known to modify it. Members of the AID/APOBEC protein family can deaminate DNA. Similarly, members of the ADAR family can deaminate RNA. Characterizing the scope of these events is challenging. Here we use large genomic data sets, such as the two billion sequences in the NCBI Trace Archive, to look for clusters of mismatches of the same type, which are a hallmark of editing events caused by APOBEC3 and ADAR. We align 603,249,815 traces from the NCBI trace archive to their reference genomes. In clusters of mismatches of increasing size, at least one systematic sequencing error dominates the results (G-to- A). It is still present in mismatches with 99% accuracy and only vanishes in mismatches at 99.99% accuracy or higher. The error appears to have entered into about 1% of the HapMap, possibly affecting other users that rely on this resource. Further investigation, using stringent quality thresholds, uncovers thousands of mismatch clusters with no apparent defects in their chromatograms. These traces provide the first reported candidates of endogenous DNA editing in human, furt