Analysis of AmpliSeq RNA-Sequencing Enrichment Panels
This study presents a proof of concept of encoding genomic signatures in the AmpliSeq technology. The samples of patients with a disease and healthy ones have been processed using an AmpliSeq RNA sequencing kit of a custom design, that include 290 amplicons, sequenced using an IonTorrent machine. The read count data show the sufficient coverage in most of the chosen amplicons, which results in a good separability between the disease patients and healthy donors. In addition, several amplicons allow for checking useful genomics variants (SNPs), whenever the coverage level permits. The paper presents a machine-learning classifier evaluation of the answer to the question of difference between the patients and healthy donors, based upon the AmpliSeq panel data. The outcome confirms the potential utility of similar RNA amplicon kits in the research and clinical practice to encode gene expression signatures of diseases and their phenotypes.
KeywordsGenomics Transcriptomics Amplicon sequencing Classification Genomic signatures
We are grateful to Kelli Bramlett, Jeoffrey Schageman, and Daniel Williams from LifeTech for discussion on AmpliSeq technology, to Andreas Tobler for coordinating the collaboration and to Marzanna Künzli-Gontarczyk, Daria Bochenek and Josias Brito Frazao for the help in the sequencing library prep and discussion on the lab aspects of the study. This work was supported by the grants Sciex.ch (nr. 11.182 to AS and MO, and nr 12.289 to MW and MO).