Quality and Value
- One error over 12 years of laboratory operation out of ~10,000 Proficiency Tests, both external and internal. For individual gene sequencing tests and panel sequencing tests, we count each exon as a Proficiency Test.
- Comparison of our Sanger sequencing to NextGen sequence data: Four errors out of 19.5 Mb sequenced (~7,400 sequence variants) (all four errors were the result of allele dropout during PCR).
- Comparison of our NextGen sequencing to Sanger sequence data and to NextGen sequence data from other labs: One error out of 7.0 Mb sequenced (~9,800 sequence variants).
- Ten specimen labeling errors out of ~45,000 opportunities, but only one of which led to an incorrect report.
- Free testing for variants of uncertain significance is provided for up to two family members of probands who were tested at PreventionGenetics.
- All of our test results and reports are carefully reviewed by at least four highly trained and experienced individuals, including two doctorate geneticists.
- Our genotyping panel is run on all specimens, as a quality control measure, to detect specimen mislabeling.
- All variants detected by NextGen sequencing that are pathogenic or of uncertain significance are confirmed by Sanger sequencing (except for uncertain variants in exome tests).
- All gene-centric aCGH results are confirmed by PCR. Breakpoints are identified in many cases through sequencing of the PCR products. We then offer more cost effective PCR tests for family studies.
- All targeted variant testing (mostly single and double exon sequencing), and prenatal testing in particular, are performed twice by different lab personnel.
- For genes which cannot be accurately analyzed by NextGen sequencing due of the presence of pseudogenes, we supplement the NextGen data with special Sanger sequencing tests. Such genes include PKD1, GBA, PMS2 and NEB.
- In our PGxome tests, for variant interpretation, we distribute the variants to our PhD and MD experts, each of whom focuses on a specific subset of the genome. This results in more efficient and accurate variant interpretation.
- We analyze all NextGen sequencing data for copy number variants (CNVs). The sensitivity of this approach for CNV detection is still lower than aCGH, but is improving.
- All sequence variants that are not common (≥ 10% allele frequency) are interpreted manually by our doctorate geneticists. We do not rely solely on automated approaches.
- Wherever practical, we utilize quantitative approaches for interpretation of sequence variants. We do not rely solely on qualitative approaches.
- We retain excess DNA from patient testing so that it is available for future testing and for quality control. This saves considerable phlebotomy and shipping costs. Patients that undergo testing at PreventionGenetics receive a discounted rate on DNA Banking.
- PreventionGenetics retains complete patient sequences for reinterpretation and to benefit family members. This data is available for eventual transfer into patient electronic health records.
- All staff who work on tests and test reports are on site in Marshfield, including our counselors and doctorate geneticists. None of these employees work remotely. This facilitates communication and continuing education.
- We are transparent with test prices on our web site.
- Special sizing assays are run for regions of short tandem repeats within or near coding regions. Examples are the (T) 9 sequence within exon 9 of the ZMPSTE24 gene and the (TG) 11 (T) 7 sequence in intron 8 of the CFTR gene. Such repeat regions cannot be accurately determined by sequencing alone.
- For chromosomal microarray tests, we routinely report candidate genes for recessive disease which lie in regions with absence of heterozygosity.
- Maternal cell contamination studies are offered at no additional cost for fetal testing.
- Where practical, we perform sequential testing for founder mutations first before completing full gene or panel sequencing to hold down costs to the patients. However, concurrent testing can be requested for time sensitive cases.
- Brief preventive medicine summaries about specific genes and associated disorders have been placed on our web site to act as resources for healthcare providers. These summaries may be particularly useful when preparing letters of medical necessity.
- We have provided all sequence variants found in our patients to the NCBI ClinVar database. We make all of our test data available for research purposes (while protecting patient confidentiality). We provide free variant interpretation for any clinically relevant gene.