RNA editing study under intense scrutiny

http://www.nature.com/news/rna-editing-study-under-intense-scrutiny-1.10217?WT.ec_id=NEWS-20120320

Today, the three groups estimate that up to 94% of the putative RNA-editing sites identified in Cheung’s paper are wrong. The groups, which worked independently, say that multiple sources of error contributed to the original paper’s overestimate of ‘RNA–DNA differences’ (RDDs). Other researchers had previously criticized Cheung's findings⁵ (see 'Estimates of errors').

Study Estimated rate of false positives Possible sources of error Lin, et al.¹ 89% mapping errors, genetic variation, gene duplications Pickrell, et al.² 88-94% sequencing errors, mapping errors, genetic variation Kleinman & Majewski³ 68-90% sequencing errors, mapping errors, genotyping errors Schrider, et al.⁵ >90% gene duplications

All three groups say that the work is riddled with errors that arose during the process of sequencing RNA fragments and mapping the reads back to their corresponding stretches of DNA. Cheung's group sequenced RNA using machines, sold by Illumina of San Diego, California, that read the sequences of short fragments of genetic material.

“These sequencing techniques are great, but you’ve really got to get to know and understand the biases and potential errors that accompany them,” says Joseph Pickrell, an evolutionary genomicist at Harvard Medical School in Boston, Mass., who co-authored the comment with Pritchard.