Fraunhofer Institute for Toxicology and Experimental MedicineTransferring single-cell genomics and single-cell transcriptomics into clinical applications requires properly adjusted quality controls. Taking into account the needs for routine diagnostic application, we developed a three-pronged quality control (QC) assay which assesses the quality of each sample amplified by the Ampli1 WGA technology prior to subjecting it to a next-generation sequencing application. The QC not only allows prediction of the genomic regions which will most likely be detected after whole-genome sequencing, but also determination of the exonic regions accessible by whole-exome sequencing. As a complement to the Ampli1 WGA QC assay we developed a three-pronged QC assay for single-cell transcriptome amplification (Ampli1 WTA) following the same principle as applied for the Ampli1 WGA QC assay.