Misattributed parentage identified through diagnostic exome sequencing: Frequency of detection and reporting practices.

Access to genetic testing, namely, diagnostic exome sequencing (DES), has significantly improved, subsequently increasing the likelihood of discovering incidental findings, such as misattributed relationships and specifically misattributed parentage (MP). Until the recently published ACMG statement, there had been no consensus for laboratories and clinicians to follow when addressing such findings. Family-based genomic testing is valuable for accurate variant interpretation but has the potential to uncover misattributed familial relationships. Here, we present the first published data on the frequency of MP identified through DES at a clinical laboratory. We also investigated clinicians' decisions on how to proceed with analysis, reporting, and disclosure. A database of 6,752 families who underwent parent-proband ('trio') DES was retrospectively reviewed for molecular identification of MP and clinicians' MP disclosure decisions. Among 6,752 trios, 39 cases of MP were detected (0.58%). Non-paternity was detected in all cases, and in one instance, non-maternity was also identified. All clinicians decided to proceed by omitting the MP individual from the analysis. Clinicians chose to proceed with duo analysis (87.2%), modify information on the report (74.4%), and communicate MP results to the mother (71.8%), suggesting a trend toward not disclosing to the putative father or proband. The data show that trio DES involves a chance of detecting MP and that clinician disclosure practices do not appear to routinely include direct disclosure to the putative father. MP identified in our parent-proband trios sent in for DES is lower than the reported frequency of MP in the general population due in part to ascertainment bias as families with known or suspected MP are presumably less likely to pursue trio testing. These data may inform laboratory policies and clinician practices for addressing incidental findings such as MP.

Exome sequencing in neonates: diagnostic rates, characteristics, and time to diagnosis.

PURPOSE: Neonatal patients are particularly appropriate for utilization of diagnostic exome sequencing (DES), as many Mendelian diseases are known to present in this period of life but often with complex, heterogeneous features. We attempted to determine the diagnostic rates and features of neonatal patients undergoing DES. METHODS: The clinical histories and results of 66 neonatal patients undergoing DES were retrospectively reviewed. RESULTS: Clinical DES identified potentially relevant findings in 25 patients (37.9%). The majority of patients had structural anomalies such as birth defects, dysmorphic features, cardiac, craniofacial, and skeletal defects. The average time for clinical rapid testing was 8 days. CONCLUSION: Our observations demonstrate the utility of family-based exome sequencing in neonatal patients, including familial cosegregation analysis and comprehensive medical review.

Prolonged cytopenia following CD19 CAR T cell therapy is linked with bone marrow infiltration of clonally expanded IFNγ-expressing CD8 T cells.

Autologous anti-CD19 chimeric antigen receptor T cell (CAR T) therapy is highly effective in relapsed/refractory large B cell lymphoma (rrLBCL) but is associated with toxicities that delay recovery. While the biological mechanisms of cytokine release syndrome and neurotoxicity have been investigated, the pathophysiology is poorly understood for prolonged cytopenia, defined as grade ≥3 cytopenia lasting beyond 30 days after CAR T infusion. We performed single-cell RNA sequencing of bone marrow samples from healthy donors and rrLBCL patients with or without prolonged cytopenia and identified significantly increased frequencies of clonally expanded CX3CR1hi cytotoxic T cells, expressing high interferon (IFN)-γ and cytokine signaling gene sets, associated with prolonged cytopenia. In line with this, we found that hematopoietic stem cells from these patients expressed IFN-γ response signatures. IFN-γ deregulates hematopoietic stem cell self-renewal and differentiation and can be targeted with thrombopoietin agonists or IFN-γ-neutralizing antibodies, highlighting a potential mechanism-based approach for the treatment of CAR T-associated prolonged cytopenia.

Quality of Clinician-Reported Cancer History When Ordering Genetic Testing.

PURPOSE: Clinical history data reported on test requisition forms (TRFs) for hereditary cancer multigene panel testing (MGPT) are routinely used by genetic testing laboratories. More recently, publications have incorporated TRF-based clinical data into studies exploring yield of testing by phenotype and estimating cancer risks for mutation carriers. We aimed to assess the quality of TRF data for patients undergoing MGPT. PATIENTS AND METHODS: Ten percent of patients who underwent hereditary cancer MGPT between January and June 2015 at a clinical laboratory were randomly selected. TRF-reported cancer diagnoses were evaluated for completeness and accuracy for probands and relatives using clinical documents such as pedigrees and chart notes as the comparison standard in cases where these documents were submitted after the time of test order. RESULTS: TRF-reported cancer sites and ages at diagnosis were complete for > 90.0% of proband cancer diagnoses overall, and the completion rate was even higher (> 96.0%) for breast, ovarian, colorectal, and uterine cancers. When reported, these data were accurate on TRFs for > 99.5% of proband cancer sites and > 97.5% of proband ages at diagnosis. Cancer site and age at diagnosis data were also complete on the TRF for the majority of cancers among first- and second-degree relatives. Completeness decreased as relation to the proband became more distant, whereas accuracy remained high across all degrees of relation. CONCLUSION: Data collected as part of cancer genetic risk assessment is completely and accurately reported on TRFs for the majority of probands and their close relatives and is comparable to information directly obtained from clinic notes, particularly for breast and other cancers commonly associated with hereditary cancer syndromes.