Citations

Abstract Background: Germline predisposition states (GPS), including inherited bone marrow failure syndromes (IBMFS) are seen in 5-10% of individuals with myeloid neoplasms (MN). Given overlap with somatic driver genes, blood, saliva, and buccal swabs are suboptimal specimens for GPS testing in MN; the latter two due to contamination with blood cells(Jerez, 2024). Skin biopsy with fibroblast culture-derived DNA remains the gold standard, but the process is expensive, takes 6-8 weeks to complete, and fibroblast culture failure can occur in some patients with telomere biology disorders. Given the need to rapidly screen donors for HSCT and adjust therapy/conditioning in certain IBMFS, we developed a rapid hematologic germline testing algorithm using hair follicle-derived DNA. Methods The study was conducted after IRB approval through the Mayo Clinic GPS/IBMFS clinic. To perform PCR-based hair follicle testing, we obtained 15-25 hair follicles (bulbs) per patient. The bulbs were placed in a microcentrifuge tube and subjected to a 24-hour digestion and extraction protocol using a modified version of the QIAGEN DNA Purification from Dried Blood Spots protocol. DNA quality was assessed by Nanodrop and Qubit.Testing included either validation of known or suspected germline variants (e.g., RUNX1, DDX41, ETV6), or panel testing (e.g., GPS or IBMFS). Pathogenic variants were validated by repeat testing in a CAP/CLIA certified lab prior to medical decision making. 23 patients underwent whole exome sequencing (WES) in a CAP/CLIA lab, and 13 patients had concurrent germline testing using alternate DNA sources (8 skin biopsies, 1 saliva, 4 buccal swabs). Results Ninety-three patients (49 male, 53%) underwent hair follicle-derived germline DNA testing (median age 63 years). Indications for germline testing included the presence of a suspected variant on somatic testing with variant allele frequency (VAF) between 35%-60% ( n= 66, 71%), patient age <50 years (n=26, 28%), antecedent thrombocytopenia (n=15, 16%), presence of syndromic features (n=4, 4%), patient history of multiple malignancies (n=4, 4%), and positive family history (n=15, 16%). Time to reporting variants after receipt of hair follicle-derived DNA was <14 days. There were zero complications associated with the procedure. DNA quality as assessed by Nanodrop revealed a median nucleic acid concentration of 25.64 ng/μL. The median A260/A280 ratio was 1.86 (range 0.701-2.133) and the median A260/A230 ratio was 1.27 (range -8.193-9.223). DNA quality was insufficient for chromosomal microarray (CMA) assessments. Of 93 patients evaluated, 67 (72%) had ≥1 germline variant, with 3 having >1 germline variant for a total of 72 variants. Pathogenic/likely pathogenic variants identified included: DDX41 (30, 41.7%), TP53 (4, 5.6%), ANKRD26 (4, 5.6%), RUNX1 (4, 5.6%), GATA2 (3, 4.2%), TERT (3, 4.2%), JAK3 (2, 2.8%), SAMD9/SAMD9L (2, 2.8%), ATM (2, 2.8%), and 1 each (1.4%) in BCL2, BCOR, BPGM, CDKN2A, CEBPA, CHEK2, CSF3R, CXCR4, DNMT3A, ETV6, GATA1, MPL, MPO, POT1, PTPN11, RPL5, and SH2B3. In the 13 patients that had concurrent germline testing, results were identical in all cases, except for 1 false negative in a buccal specimen (PTPN11) and 1 case of germline mosaicism, where the TP53 variant was identified in the blood and hair follicle DNA but not in skin fibroblast DNA. After testing, 30 (44.7%) patients had a change in their management plan: 8 (27%) with DDX41-GPS were observed due to known latency of DDX41-mutant MN, 6 (20%) were referred for HSCT based on the germline variant (CEBPA, DDX41, GATA1, GATA2, RPL5, TP53), 6 (20%) were placed on an enhanced surveillance plan for cancer screening (1 ANKRD26, 3 TERT, 2 TP53), 4 (13%) patients undergoing HSCT had related donors removed from consideration as they were carriers (2 DDX41, 1 ANKRD26, and 1 SAMD9), 2 (7%) patients with neutropenia and underlying germline variants (1 ATM, 1 DDX41) had G-CSF therapy discontinued due to concerns for clonal stimulation, and 1 (3%) patient with a germline CDKN2A mutation (hematological diagnosis- CMML) was recommended to avoid radiation therapy for prostate cancer. Conclusion In summary, we validate a rapid and simple hair follicle-derived DNA based germline assessment for patients with hematological disorders and demonstrate a positive impact on clinical care in 44% of patients. We are currently optimizing DNA quality so that germline copy number alterations can be better detected using CMA.

Context.— Clinical laboratories are increasingly implementing pharmacogenomic (PGx) testing. Although PGx is similar to genetic testing for other indications, there are unique aspects that laboratories should consider. Objective.— To aid clinical laboratories that are implementing clinical PGx testing by describing characteristics of PGx test design and validation, as well as approaches to reporting. Resources that are useful for clinical laboratories performing PGx testing will be highlighted. Design.— The College of American Pathologists formed a workgroup composed of laboratorians with expertise in clinical PGx testing. The workgroup included representatives from the Association for Molecular Pathology and the American College of Medical Genetics and Genomics. The workgroup reviewed pertinent literature, as well as experience from proficiency testing and from members’ laboratories. Results.— The workgroup recommends that laboratories implementing PGx consider the following concepts: testing platform, test design (ie, selection of pharmacogenes and variants/alleles), use of reference materials during test development and as controls during clinical runs, star allele and standard nomenclature systems, translations from genotype to predicted phenotype, and considerations for result reporting including making medication recommendations. The workgroup provides considerations when using report vendors, emphasizing the clinical laboratory’s role and responsibility when implementing such reporting tools from vendors. Conclusions.— Clinical laboratories should be familiar with the fundamentals of PGx, ensure that PGx testing meets the applicable regulatory requirements for all aspects of the clinical laboratory testing process, and follow recommendations for standardization of nomenclature and reporting.

Abstract Description Hematopoiesis declines with age due to intrinsic and extrinsic dysregulation resulting in diminished lymphopoiesis. Hoxa9 is a pleiotropic hematopoietic regulator necessary for stem/progenitor cell (HSPC) maintenance and lymphoid differentiation. Interestingly, bone marrow (BM) HSPC and B lineage compartments of young hoxa9-/- mice mimic that which accompanies aging. Hoxa9 is a negative regulator of p16ink4a, a cyclin-dependent kinase inhibitor upregulated in hoxa9-/- HSPCs and a gatekeeper of the G1 to S cell cycle checkpoint. We hypothesized that increased expression of p16ink4a contributes to the HSPC and/or B progenitor alterations due to hoxa9-deficiency. Interestingly, BM B lymphopoiesis was normalized in hoxa9-/-p16ink4a-/- (DKO) mice, but alterations were less obvious in HSPCs. Flow analysis of the HSPC compartment proliferation showed contraction of unbiased but not myeloid-biased progenitors prior to lineage fate commitment. hoxa9-/- CFU-PreB were blunted then rescued by p16ink4a co-ablation. Primary BM transplant demonstrates DKO like hoxa9-/- has reduced reconstitution efficiency but differs with superior B lineage reconstitution similar to controls. Bioinformatic analysis of recent open access CUT&RUN data in HSPCs confirms Hoxa9 binds promoters in genes relevant to G1 to S cell cycle checkpoint, these findings currently being validated. Our work emphasizes HSPC regulatory factors as crucial targets in combating age-associated maladies of the immune system. Funding Sources Supported by NIH R01AG076163 Topic Categories Hematopoiesis and Immune System Development (HEM)

Abstract Molecular profiling reveals that up to 40% of advanced biliary tract cancers (BTCs) harbor actionable genomic alterations amenable to matched targeted therapies. However, conventional trial designs typically evaluate these agents in pretreated populations, resulting in approvals for later-line use. Notably, 25–44% of patients with advanced BTC may become ineligible for treatment after first-line therapy due to disease progression or functional decline, thus the real-world survival outcomes with matched therapies remains poorly characterized. This international collaborative study includes data from Mayo Clinic, Duke Cancer Institute, and National Cancer Center East (Japan), as well as a combined dataset from the SCRUM-Japan GOZILA, MONSTAR-SCREEN-1, and MONSTAR-SCREEN-2 projects. We assessed overall survival (OS) of patients based on the presence of actionable alterations and the receipt of matched therapy. To adjust for confounding, we applied propensity score weighting with inverse probability of treatment and multivariate Cox regression modeling, controlling for age, sex, tumor location, prior resection, and mutational subgroup. Among 1,049 patients that were analyzed, 358 (34.1%) harbored actionable alterations, with 160 (44.7%) receiving matched targeted therapy. The matched group (patients with actionable tumors who received a matched therapy) were significantly associated with longer median OS (23.3 months; 95% CI: 19.5–30.4) compared to the unmatched group (14.7 months; 95% CI: 12.8–17.9) and those with non-actionable tumors (17.1 months; 95% CI: 15.5–18.7; HR 0.57, 95% CI: 0.46–0.71; p < 0.0001). The unmatched group also was associated with the lowest three-year OS rate (13% vs. 35% in matched and 19% in actionable groups, respectively; p<0.0001). On multivariable analysis with patients who received ≥2 lines of therapy, receipt of matched therapy remained an independent predictor of improved OS (HR 0.62; 95% CI 0.43–0.90). These findings support the early integration of targeted therapies in BTC management and underscore the need to overcome systemic barriers to treatment access.

Background and Purpose Informed consent (IC) practices for endovascular thrombectomy (EVT) in acute stroke are not well elucidated. We investigated the roles and specialties of those obtaining EVT IC, aiming to provide insights for enhancing the process. Methods We conducted a survey from July- December 2023 among acute stroke care clinicians. Utilizing Qualtrics, we disseminated a questionnaire through various national and international online platforms. This analysis summarizes the characteristics of individuals who obtain IC at respondents’ institution. Results Among 168 respondents, 71% were staff physicians, 70% practiced in the US and 70% worked at academic centers. Neurology (77%) was the most common specialty obtaining EVT IC, followed by neurosurgery (41%), radiology (30%) and emergency medicine (EM) (10%). Staff physicians were the most frequently involved (61%), followed by fellows (43%), residents (48%) and advanced practice providers (APPs) (36%). Comparatvely, non-US institutions were more likely to utilize neurologists alone (50% vs 31%, P = 0.016) and staff physicians (76% vs 54%, P = 0.008), while US institutions more often utilized neurosurgeons (51% vs 18%, P < 0.001), APPs (43% vs 18%, P = 0.002) and residents (56% vs 28%, P = 0.001). Non-academic institutions used EM (25% vs 5%, P < 0.001) and APPs (50% vs 31%, P = 0.031), while academic institutions commonly utilized neurosurgeons (48% vs 18%, P = 0.001), residents (59% vs 13%, P < 0.001) and fellows (52% vs 18%, P < 0.001). Conclusion Neurologists and staff physicians are the primary providers obtaining EVT IC, with variations based on region and institution type. Future efforts to optimize the IC process should integrate various specialties and be widely adaptable.

Pharmacogenomics (PGx) has the potential to improve prescribing practices. In 2012, our institution developed a multidisciplinary program to implement PGx-CDS to support the clinical practice. CDS has been implemented for 45 drug-gene interactions, in 42,000 patients with PGx tests results, and in 2023, approximately 9281 CDS interventions have triggered at the time of prescribing. The program has been successful.

Abstract Endoscopic mucosal resection (EMR) techniques for large (≥20 mm) nonpedunculated colorectal polyps (LNPCPs) have expanded with the introduction of ablation and cold EMR. This study assessed adverse events (AEs) for the newer EMR techniques, including cold EMR, compared with hot EMR. We conducted a secondary analysis of four prospective multicenter studies of consecutive patients with LNPCPs undergoing EMR from 2019 to 2024. The primary outcome was serious AEs (SAEs) with cold and hot EMR. Secondary outcomes included SAEs in the hot EMR subgroups (no ablation [hEMR], margin ablation [hEMR-m], margin and base ablation [hEMR-mb]). 1762 patients (mean age 65.8; 1890 LNPCPs) were included: 522 cold and 1368 hot EMRs (368 hEMR, 770 hEMR-m, 230 hEMR-mb). SAEs were higher with hot EMR (4.7%, 95%CI 3.6%–5.9%) vs. cold EMR (1.9%, 95%CI 0.9%–3.5%), also for the subgroups of hEMR (6.0%, 95%CI 3.8%–8.9%), hEMR-m (3.9%, 95%CI 2.6%–5.5%), and hEMR-mb (5.2%, 95%CI 2.7%–8.9%). Serious postendoscopic bleeding (PEB) was numerically higher with hot EMR (2.3%, 95%CI 1.6%–3.3%) vs. cold EMR (1.3%, 95%CI 0.5%–2.7%), also for the subgroups of hEMR (3.0%, 95%CI 1.5%–5.3%), hEMR-m (1.9%, 95%CI 1.1%–3.2%), and hEMR-mb (2.6%, 95%CI 1.0%–5.6%). Perforation, intraprocedural and post-procedural, was numerically higher with hot EMR (1.2%, 95%CI 0.7%–2.0%) vs. cold EMR (0.2%, 95%CI 0.0%–1.1%). hEMR-m and hEMR-mb with clipping had lower rates of serious and overall PEB than no clipping. Cold EMR demonstrated lower rates of SAEs, serious PEB, and perforation compared with hot EMR. Perforation and mortality occurred almost exclusively after hot EMR. Hot EMR with margin +/− base ablation did not increase SAEs compared with hot EMR without ablation.

ABSTRACT Major depressive disorder (MDD) is a substantial public health challenge. Pharmacogenomics (PGx), which identifies genetic variations that predict drug treatment outcomes, may have utility for clinical practice, but adequate representation of all populations is needed. As precision medicine in psychiatry moves towards the use of Artificial Intelligence (AI) and Machine Learning (ML) to predict treatment outcomes using PGx data, representation of diverse populations will be especially important in order to mitigate algorithmic bias and achieve equitable and generalizable findings. This work sought to quantify population diversity in pharmacogenomic studies of MDD through a systematic review. Data from 390 MDD antidepressant PGx studies were extracted from 5739 articles screened. Studies summarized were predominantly conducted in Europe, East Asia, and North America. Across all global studies, the study population comprised 57.3% White, 36.4% Asian, 1.7% Black, 3.5% Hispanic/Latino, and 0.1% Native American or Indigenous participants. Only sixty‐three (16.2%) studies included Black or Latino/Hispanic patients. Additionally, Black, Asian, Hispanic/Latino, and American Indian/Alaska Native populations were statistically underrepresented in U.S. study populations when compared to national census data, while Asian and Black populations were underrepresented in the United Kingdom. The overrepresentation of participants from a limited number of countries combined with the underrepresentation of Black and Hispanic/Latino populations could impact the extent to which pharmacogenomic testing and associated AI/ML‐based PGx tools could individualize antidepressant medication regimens for treating MDD.