Skip links

Chimerism Testing

Chimerism testing (engraftment analysis) is performed for patients who have received a hematopoietic stem cell transplant. The test involves identifying the genetic profiles of the recipient and of the donor and then evaluating the extent of mixture in the recipient’s blood or bone marrow. First, DNA is isolated from the recipient and potential donor before the transplant and analysis is performed to determine whether the genetic markers unique to the donor and the recipient have sufficient power to distinguish the donor from the recipient. Next, after the transplant takes place, the performance of the transplant engraftment is assessed by evaluating the donor versus recipient contribution of white blood cells in post-transplant blood or bone marrow specimens obtained from the recipient.

  • The DNA is isolated from the recipient, donor, and post-transplant samples.
  • DNA is amplified via the Promega GenePrint24 System which employs methodology commonly used in human identity testing and is accomplished by the analysis of genomic polymorphisms called short tandem repeat (STR) loci.
  • The percent donor chimerism is calculated and reported, and a longitudinal plot of historic data is generated for successive post-transplant specimens.

Prosigna Assay

The Prosigna™ Breast Cancer Prognostic Gene Signature Assay (formerly called the PAM50 test) is an in vitro diagnostic assay performed using FFPE breast tumor tissue previously diagnosed as invasive breast carcinoma. This qualitative assay utilizes gene expression data, weighted together with clinical variables to generate a risk category and numerical score, to assess a patient’s risk of distant recurrence of disease.

Indications for testing:

The Prosigna Breast Cancer Prognostic Gene Signature Assay is indicated for use in postmenopausal women with hormone receptor–positive, node-negative or node-positive early-stage (stages I and II) breast cancer to be treated with adjuvant endocrine therapy

Test outputs for risk assessment:

1- Prosigna Score: Derived from a proprietary algorithm based on the PAM50 gene signature, the Prosigna Score is a numerical value on a 0 to 100 scale that correlates with the probability of distant recurrence within 10 years

2- Risk group: Based on the Prosigna Score and nodal status, risk classification is provided to allow interpretation of the Prosigna Score by using cutoffs related to clinical outcome in tested patient populations

Distant recurrence-free survival (DRFS) rates are significantly different among risk groups:

In node-negative patients, the 10-year DRFS rates were >95% for the low-risk group, 90.4% for the intermediate-risk group, and <85% for the high-risk group

In node-positive patients, the 10-year DRFS rates were 94.2% for the low-risk group and 75.8% for the high-risk group.

Exome Sequencing

  • CES is a test that examines the portion of the genome that encodes for proteins (exons) and their flanking splice junctions.
  • CES aims to identify disease-causing variants within the exons.
  • CES interprets the identified variants within the context of the clinical presentation in order to reach a diagnosis for patients with challenging undiagnosed genetic disorders.
  • The UAGC-CS sequences full trio or proband-only exomes encompassing over 50MB of around 21,000 human genes.
  • Patients are sequenced to a depth greater than 50X coverage on a Illumina HiSeq 2500 and all data is aligned and mapped back to the human reference genome.
  • The UAGC-CS clinical report includes all validated de novo variants as well as alternate alleles found in the patient sample prioritized by known or potential pathogenicity and relation to the clinical phenotype.
  • Incidental findings are also reported if patient is consented to receive such findings.
  • Genetic counseling before and after testing is required.