Fast turn-around time of an assay like UDT-Seq is important for its clinical implementation. The sequencing presented above requires approximately 12 days of an Illumina GAII run to complete. Recent technology developments have resulted in the commercialization of new, smaller instruments that are time- and cost-effective while still providing a sufficient yield compatible with UDT-Seq breadth and depth. Using multiplexing adapters, we sequenced the same four calibration samples (CAL-A to CAL-D) in one run of Illumina MiSeq (Materials and methods). This resulted in an average depth of 1,571× per amplicon. Using an analysis strategy strictly identical to the one described for the GAII data, we noticed a significant reduction of the substitution rate, especially at the end of the reads for 'A' and 'T' reference bases (Figure S8a-d in Additional file 1). These improvements are the consequence of a better chemistry since the initial GAII run as well as faster cycling time. This resulted in a more than six-fold reduction in the number of positions determined as significantly noisy by filter 7 (Figure S8e in Additional file 1). As a
