Lynch syndrome is characterized by familial predisposition to cancers of the colon, endometrium, ovary, stomach, and urinary tract. 4–11% of cases are caused by variants in PMS2. Testing for inherited PMS2 variants is hampered by a pseudogene, PMS2CL, which has nearly identical homology to PMS2 in exons 12–15 of the gene. Therefore, it is difficult to determine if a variant is in PMS2 or PMSCL and different and innovative methods are needed for analysis of this region.
Erin O’Leary, MS, LCGC discusses Invitae’s methods to disambiguate variants detected in PMS2 exons 12–15. Variant interpretation in this region of PMS2 is highly dependent on laboratory methods. Therefore, a laboratory’s technology and methods are crucial in avoiding misdiagnoses of Lynch syndrome and inappropriate management.
Next-generation sequencing (NGS) technology with deep sequencing coverage enhances sensitivity to detection and allows identification allele balances suggestive of low-level mosaicism that was recently undetectable by Sanger sequencing. Detection of a mosaic variant in a patient being tested for an inherited cancer predisposition poses challenging considerations for clinical interpretation and genetic counseling.
To facilitate understanding of the clinical manifestations, this presentation describes the causative biologic events underlying germline, somatic, and gonosomal constitutional mosaicism. Because a finding of mosaicism in the peripheral blood may have prognostic significance related to risk for development of a hematopoietic malignancy, the presentation explores the concept and criteria for the newly proposed entity of “clonal hematopoiesis of indeterminate significance” and discusses the role of TP53 mutations in the origin and evolution of selected clones with increased neoplastic potential created secondary to cytotoxic chemotherapy and/or radiotherapy exposure.
Follow-up clinical management recommendations are presented that can be used when a mosaic variant is unexpectedly found in the peripheral blood. Finally, because mosaic findings are expected and can affect inherited genetic disease testing in patients with known hematopoietic malignancies, the presentation also covers important considerations for clinical interpretation, including limitations to testing in patients testing with known circulating hematopoietic neoplasms.
What does it mean to be a gold standard in genetic testing? At Invitae, we believe there’s a new gold standard today, one that includes both high quality testing and a dedication to improving medicine through data sharing.
In this webinar, Steve Lincoln, head of scientific affairs at Invitae, discusses ways in which you can make sure the testing you provide your patients meets a high standard of excellence.
Invitae’s philosophy is to combine thoroughly validated analysis with a dedication to submitting our variant interpretations into the public domain. In this way we are setting a new gold standard.
Sequencing the PMS2 gene is difficult. Accurately analyzing complex portions of this gene for sequence and del/dup variants usually requires expensive and complex lab techniques. We have developed a method for full PMS2 sequencing and deletion/duplication analysis that offers both the same high quality and the same affordable price you’ve come to expect from Invitae.
Our new, highly accurate method covers both PMS2 and its pseudogene, PMS2CL. The trick lies in evaluating all reads from both genes as if they belonged only to PMS2, and then using a bioinformatic screen to call variants across this region. In cases where no variants are found, the sample can continue through the testing process. In cases with positive screen findings, we use alternate technologies to determine whether the variant is in PMS2 or PMS2CL.
Join our webinar to learn about Invitae’s innovative approach to PMS2 exons 12-15, including how we thoroughly validated this process.