Gilmer, Heather C. Flynn

Abstract Background X and Y chromosome analysis is a critical component of genetic testing, used both diagnostically and as a quality control (QC) metric. Discordances between expected and observed sex chromosome data can arise due to mislabeling, demographic data errors, transplant history, or biological variations. Such discordances pose challenges to laboratories and affect patient care, particularly in marginalized populations and unique clinical contexts. Methods We reviewed cases of sex chromosome discordance identified at our laboratory from January 2021 through August 2023. Cases spanned various testing methods and were categorized by the root cause, including mislabeling, sample mix-ups, transgender individuals, stem cell transplants, and unexplained causes. Case outcomes were assessed, and potential resolutions were analyzed. Results Among 65 cases identified, the leading cause of discordance was mislabeling (n = 20, 31%), followed by other/not identified (n = 16, 25%), sample mix-ups (n = 13, 20%), transgender individuals (n = 9, 14%), and stem cell transplants (n = 7, 11%). Cases required additional QC processes such as reanalysis, clinician contact, and occasionally sample re-collection. The process extended turnaround times by up to 13 business days. Detailed case reviews highlighted the challenges and implications of managing these discordances, emphasizing the importance of accurate data transmission and inclusive practices. Conclusion Using X and Y chromosome data as a QC metric can identify critical errors but also introduces limitations and bias. Improved standardization, inclusive practices, and alternative QC methods are necessary to ensure accuracy and equitable patient care. Collaborative efforts are required to address demographic complexities and reduce testing delays.

Abstract BACKGROUND: DNA rearrangements that result in the inappropriate activation of the PDGFRA gene at 4q12 and the PDGFRB gene at 5q31-q33 occur rarely in patients with chronic myeloproliferative disorders. Approximately 10% of patients with systemic mast cell disease/hypereosinophilic syndrome have a unique mutational mechanism resulting in PDGFRA overexpression due to a novel microdeletion of the CHIC2 region resulting in the juxtaposition of FIP1L1 and PDGFRA. PDGFRB activation has been observed in patients with chronic myelomonocytic leukemia/atypical chronic myeloid leukemia and has been associated with 11 translocation partners. Since patients with demonstrable breakpoints in the PDGFRA and PDGFRB genes often have a dramatic disease response to the tyrosine kinase inhibitor imatinib, we searched the Mayo Clinic Cytogenetic database to identify additional translocation partners involving these regions. METHODS: Homebrew dual-color FISH probes were created which flank the PDGFRA gene at 4q12 and the PDGFRB gene at 5q31-q33. Archived bone marrow karyotypes analyzed in the Mayo Clinic Cytogenetics laboratory from a 15 year period (1989-2004) were reviewed to determine the frequency of specimens with breakpoints at 4q12 and 5q31-33. Of the 29,047 abnormal specimens, 64 possessed a 4q12 breakpoint and 164 possessed a 5q31-q33 breakpoint (excluding simple deletions). Of these 228 patients, residual bone marrow specimens were available from 170 patients for FISH analysis. RESULTS: Eleven of 50 patients with a 4q12 breakpoint yielded a break with the PDGFRA FISH probe. Eight patients had the previously described t(4;12)(q12;p13) which results in a reciprocal exchange between the TEL oncogene and has a break near, but not within, the PDGFRA gene. Three patients had breaks within the PDGFRA gene and had novel translocation partners including 1q44, 3q25 and 17q23. Twelve of 120 patients with a 5q31-q33 anomaly had a break detected with the PDGFRB FISH probe. Nine patients had the classic t(5;12)(q33;p13) involving PDGFRB and TEL. Three patients had novel PDGFRB translocation partners, including 1q21, 14q32 and 16p13.1. CONCLUSIONS: Breakpoints involving the PDGFRA and PDGFRB genes appear to be quite uncommon as only 23 patient samples were abnormal in our series of 29,407 abnormal bone marrow samples. With the description of three new translocations involving PDGFRB, at least 14 unique translocation partners have been identified with this gene. With the exception of the recurrent t(5;12) between PDGFRB and TEL, most translocations involving PDGFRB appear to be unique. The microdeletion of CHIC2 at 4q12 resulting in the juxtaposition of FIP1L1 and PDGFRA has been the sole mechanism thus far described resulting in the activation of this gene. The identification of the three translocations involving the PDGFRA gene represent the first classic cytogenetically visible rearrangements involving this novel gene region. While rare, we propose that all chromosome anomalies identified with breakpoints in the 4q12 and 5q31-q33 regions should receive appropriate FISH testing to determine the potential involvement of the PDGFRA and PDGFRB genes.