Quality and Value at PreventionGenetics

Since the founding of our laboratory in 2004, the leaders of PreventionGenetics have emphasized test quality. “Get the Tests Right” is our mantra. Over the years we have labored to earn a strong reputation throughout our industry for quality.

Proficiency Testing

These days, PreventionGenetics performs Proficiency Testing (PT) continuously throughout the year. We perform PT through exchange of specimens with other labs, by repeat testing of internal specimens, by utilization of specimens and data from the National Institute of Standards and Technology (NIST) Genome in a Bottle, and by participation in PT administered by the College of American Pathologists (CAP).

Our PT record is exceptional. As an example, our CAP PT results from the last three years are shown in the bar plot. This plot was taken directly from the CAP web site; it was not constructed at PreventionGenetics. The blue bars are PreventionGenetics’ results. The orange and silver bars are average results from other labs. PreventionGenetics significantly and consistently outperforms other labs.

Special Features of our Testing

We routinely incorporate many special features into our testing process to ensure quality. A few examples follow. Other labs offer some of these features, but none offers all of them.

  • Our genotyping panel is run on all specimens as a quality control measure to detect specimen mislabeling, specimen contamination, and to confirm family relationships.
  • All of our test results and reports are carefully reviewed by four highly trained and experienced individuals, including two doctorate geneticists.
  • All structural variants, including copy number variants (CNVs), that are called through analysis of the NextGen sequencing data are confirmed by a second method such as aCGH or PCR before reporting.
  • We have carefully and independently evaluated all genes for copy number. Those genes which are present in more than one copy in the haploid genome (paralogous genes) and that cannot be accurately sequenced by standard NextGen sequencing methods are treated specially. Examples include PKD1, GBA, PMS2, and NEB. In many cases, we have developed unique assays to enable us to accurately test these genes.
  • All nucleotide substitution variants that do not meet our very stringent quality criteria are confirmed by Sanger sequencing before reporting. Our sequencing error rate is ~ 10-7.
  • We take exceptional measures to avoid internal specimen mislabeling. Out of ~150,000 test reports, only one needed to be corrected because of a mislabeling error.
  • All small deletion and insertion variants are confirmed by Sanger sequencing before reporting.
  • 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.

Value

  • PreventionGenetics retains complete patient sequence information for reinterpretation and to benefit family members. This data is available for eventual transfer into patient electronic health records.
  • For our PGxome® and PGnomeTM tests, we offer one free reinterpretation of the data within three years of the test date.
  • Free testing for variants of uncertain significance is provided in up to two family members of probands who were tested at PreventionGenetics.
  • PreventionGenetics runs an outstanding clinical DNA Banking service.

Service & Expertise

  • In our PGxome® and PGnomeTM tests, we distribute the rare variants to all our PhD geneticists for interpretation. Each of these geneticists concentrates on a limited portion of the genome and becomes expert on their genes and associated disorders. In this way, we provide the best possible variant interpretation.
  • We provide free interpretation for any sequence variant in any clinically relevant gene through our Variant Interpretation Service.
  • We make all of our test data available for non-profit research purposes (while protecting patient confidentiality).
  • Many of our geneticists participate in ClinGen expert gene/variant curation groups. We have deposited many of our variant interpretations into ClinVar and will contribute more in future.
  • Although we utilize several computer programs and many databases, ultimately, sequence variants are interpreted manually by our expert PhD geneticists. We do not rely solely on automated approaches.
  • Nearly all staff who work on tests and test reports are on site in Marshfield, including our counselors and doctorate geneticists. This facilitates communication and continuing education.
  • We are transparent with test prices. All test prices are listed on our web site.