Pilot Genomic Test Service
To show whether tissue or biofluid specimens meet quality limits for genomic analysis, UNITS offers a Pilot Genomic Test Service. A representative number of specimens are submitted for analysis and a report is issued describing key quality features.
Submitted specimens should reflect the pre-analytic characteristics that are relevant to the clinical trial (i.e. method of collection, processing and storage). UNITS will use an appropriate Standard Operating Procedure to analyze the specimens (e.g. pathologist reviews and confirms cancer is present by microscopy and serial sections are macrodissected and analyzed for DNA, RNA or microRNA sequences).
List of Quality Indicators
- Lesion visible in both H&Es flanking serial unstained sections of tissue to harvest, performed by a pathologist
- Square area circled for macrodissection, in mm
- % malignant cells in circled area, performed by a pathologist
- Amplification of small versus large target segment, expressed as delta Ct value, reflecting quantity and intactness of extracted DNA or cDNA
- Bioanalyzer result on library prep, reflecting amplicon lengths and quantity
- % mapped reads and off-target reads
- Coverage for pertinent target gene segments
- Reproducibility of variant calls, allele frequency, and coverage in replicate tests of the same specimen, starting with tissue
- Each of ten polymorphic “identifier” SNPs is either homozygous at allele frequency <10% or >90%, or heterozygous at 50% +/-10% in accordance with Hardy-Weinberg equilibrium and adequate cell sampling
- Lesions claimed to be from the same patient have the same genotype at all ten identifier loci