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Sequencing artifacts in the type A influenza databases and attempts to correct them

Permanent URL:
http://handle.nal.usda.gov/10113/60131
File:
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Abstract:
Background: There are over 276 000 influenza gene sequences in public databases, with the quality of the sequences determined by the contributor. Objective: As part of a high school class project, influenza sequences with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these sequences would have an error. Students contacted sequence submitters alerting them of the possible sequence issue(s) and requested they the suspect sequence (s) be correct as appropriate. Methods: Type A influenza viruses were screened, and gene segments longer than the accepted size were identified for further analysis. Attention was placed on sequences with additional nucleotides upstream or downstream of the highly conserved noncoding ends of the viral segments. Results and Conclusions: A total of 1081 sequences were identified that met this criterion. Three types of errors were commonly observed: non-influenza primer sequence wasn’t removed from the sequence; PCR product was cloned and plasmid sequence was included in the sequence; and Taq polymerase added an adenine at the end of the PCR product. Internal insertions of nucleotide sequence were also commonly observed, but in many cases it was unclear if the sequence was correct or actually contained an error. A total of 215 sequences, or 22.8% of the suspect sequences, were corrected in the public databases in the first year of the student project. Unfortunately 138 additional sequences with possible errors were added to the databases in the second year. Additional awareness of the need for data integrity of sequences submitted to public databases is needed to fully reap the benefits of these large data sets.
Author(s):
David L. Suarez , Nikki Chester , Jason Hatfield
Note:
USDA Scientist Submission
Source:
Influenza and other respiratory viruses 2014 July v.8 no.4
Language:
English
Year:
2014
Collection:
Journal Articles, USDA Authors, Peer-Reviewed
Rights:
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.