Confirmation of Insertion, Deletion, and Deletion-Insertion Variants Detected by Next-Generation Sequencing.

BACKGROUND: Despite clinically demonstrated accuracy in next generation sequencing (NGS) data, many clinical laboratories continue to confirm variants with Sanger sequencing, which increases cost of testing and turnaround time. Several studies have assessed the accuracy of NGS in detecting single nucleotide variants; however, less has been reported about insertion, deletion, and deletion-insertion variants (indels). METHODS: We performed a retrospective analysis from 2015-2022 of indel results from a subset of NGS targeted gene panel tests offered through the Mayo Clinic Genomics Laboratories. We compared results from NGS and Sanger sequencing of indels observed in clinical runs and during the intra-assay validation of the tests. RESULTS: Results demonstrated 100% concordance between NGS and Sanger sequencing for over 490 indels (217 unique), ranging in size from 1 to 68 basepairs (bp). The majority of indels were deletions (77%) and 1 to 5 bp in length (90%). Variant frequencies ranged from 11.4% to 67.4% and 85.1% to 100% for heterozygous and homozygous variants, respectively, with a median depth of coverage of 2562×. A subset of indels (7%) were located in complex regions of the genome, and these were accurately detected by NGS. We also demonstrated 100% reproducibility of indel detection (n = 179) during intra-assay validation. CONCLUSIONS: Together this data demonstrates that reportable indel variants up to 68 bp can be accurately assessed using NGS, even when they occur in complex regions. Depending on the complexity of the region or variant, Sanger sequence confirmation of indels is usually not necessary if the variants meet appropriate coverage and allele frequency thresholds.

Implementation of preemptive DNA sequence-based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study.

PURPOSE: The Mayo-Baylor RIGHT 10K Study enabled preemptive, sequence-based pharmacogenomics (PGx)-driven drug prescribing practices in routine clinical care within a large cohort. We also generated the tools and resources necessary for clinical PGx implementation and identified challenges that need to be overcome. Furthermore, we measured the frequency of both common genetic variation for which clinical guidelines already exist and rare variation that could be detected by DNA sequencing, rather than genotyping. METHODS: Targeted oligonucleotide-capture sequencing of 77 pharmacogenes was performed using DNA from 10,077 consented Mayo Clinic Biobank volunteers. The resulting predicted drug response-related phenotypes for 13 genes, including CYP2D6 and HLA, affecting 21 drug-gene pairs, were deposited preemptively in the Mayo electronic health record. RESULTS: For the 13 pharmacogenes of interest, the genomes of 79% of participants carried clinically actionable variants in 3 or more genes, and DNA sequencing identified an average of 3.3 additional conservatively predicted deleterious variants that would not have been evident using genotyping. CONCLUSION: Implementation of preemptive rather than reactive and sequence-based rather than genotype-based PGx prescribing revealed nearly universal patient applicability and required integrated institution-wide resources to fully realize individualized drug therapy and to show more efficient use of health care resources.

Targeted Genotyping in Clinical Pharmacogenomics: What Is Missing?

Clinical pharmacogenomic testing typically uses targeted genotyping, which only detects variants included in the test design and may vary among laboratories. To evaluate the potential patient impact of genotyping compared with sequencing, which can detect common and rare variants, an in silico targeted genotyping panel was developed based on the variants most commonly included in clinical tests and applied to a cohort of 10,030 participants who underwent sequencing for CYP1A2, CYP2C19, CYP2C9, CYP2D6, CYP3A4, CYP3A5, DPYD, SLCO1B1, TPMT, UGT1A1, and VKORC1. The results of in silico targeted genotyping were compared with the clinically reported sequencing results. Of the 10,030 participants, 2780 (28%) had at least one potentially clinically relevant variant/allele identified by sequencing that would not have been detected in a standard targeted genotyping panel. The genes with the largest number of participants with variants only detected by sequencing were SLCO1B1, DPYD, and CYP2D6, which affected 13%, 6.3%, and 3.5% of participants, respectively. DPYD (112 variants) and CYP2D6 (103 variants) had the largest number of unique variants detected only by sequencing. Although targeted genotyping detects most clinically significant pharmacogenomic variants, sequencing-based approaches are necessary to detect rare variants that collectively affect many patients. However, efforts to establish pharmacogenomic variant classification systems and nomenclature to accommodate rare variants will be required to adopt sequencing-based pharmacogenomics.

The "Little MonSta" Deep-Sea Benthic, Precision Deployable, Multi-Sensor and Sampling Lander Array.

The "Little MonSta" benthic lander array consists of 8 ROV-deployable (remotely operated vehicle) instrumented lander platforms for monitoring physical and chemical oceanographic properties and particle sampling developed as part of the MMMonKey_Pro program (mapping, modeling, and monitoring key processes and controls in cold-water coral habitats in submarine canyons). The Little MonStas offer flexible solutions to meet the need to monitor marine benthic environments during a historically unprecedented time of climate-driven oceanic change, develop an understanding of meso-scale benthic processes (natural and man-made), and to calibrate geological environmental archives. Equipped with acoustic Doppler current profilers (ADCPs), sediment traps, nylon settlement plates and homing beacons, the compact and upgradable lander platforms can be deployed by ROVs to precise locations in extreme terrains to a water depth of 3000 m. The array allows cluster-monitoring in heterogeneous environments or simultaneous monitoring over wider areas. A proof-of-concept case study was presented from the cold-water coral habitable zone in the upper Porcupine Bank Canyon, where the Little MonStas collected 868.8 h of current speed, direction, temperature, and benthic particulate flux records, as well as 192 particle samples subsequently analyzed for particular organic carbon (POC), lithic sediment, live foraminifera, and microplastics. The potential to upgrade the Little MonStas with additional sensors and acoustic releases offers greater and more flexible operational capabilities.

Influence of benthic currents on cold-water coral habitats: a combined benthic monitoring and 3D photogrammetric investigation.

Strong currents are a key component of benthic habitats by supplying food and nutrients to filter-feeding organisms such as cold-water corals. Although field measurements show that cold-water coral habitats exist in areas of elevated bottom currents, flume studies show that cold-water corals feed more effectively at lower flow speeds. This research aims to explore this disconnect in situ by utilising high spatial resolution ROV photogrammetric data coupled with high temporal resolution in situ acoustic doppler current profile measurements at seven study sites within the upper Porcupine Bank Canyon (uPBC), NE Atlantic. Object-based image analysis of photogrammetric data show that coral habitats vary considerably within the upper canyon. Although there is a regional hydrodynamic trend across the uPBC, this variation is likely driven locally by topographic steering. Although live coral tends not to face directly into the prevailing current direction, preferring lower local flows speeds, they can tolerate exposure to high-flow speeds of up to 114 cm s-1, the highest recorded in a Desmophyllum pertusum habitat. Not only do these high flow speeds supply food and nutrients, they may also help contribute to coral rubble production through physical erosion. These results can be incorporated into simulations of future deep-water habitat response to changing environmental conditions while extending the upper current speed threshold for cold-water corals.

The Obesity Paradox Is Not Observed in Critically Ill Patients on Early Enteral Nutrition.

OBJECTIVES: To investigate the association between body mass index and mortality in a large, ICU population and determine if the relationship is observed among a subgroup of patients ordered early enteral nutrition. DESIGN: Retrospective cohort study within a national clinical mixed ICU database of patients admitted between January 1, 2008, and June 30, 2015. SETTING: Initial ICU admissions among patients monitored by tele-ICU programs and recorded in the Philips eICU Research Institute database. PATIENTS: A total of 1,042,710 adult patient stays with ICU length of stay more than 24 hours, of which 74,771 were ordered enteral nutrition within the first 48 hours. INTERVENTION: None. MEASUREMENTS AND MAIN RESULTS: Patient stays from 409 ICUs were included. The average age, Acute Physiology and Chronic Health Evaluation IV score, and hospital mortality were 63.6 years, 56.7, and 9.0%, respectively. Hospital mortality among body mass index categories was estimated by multivariable modified Poisson regression models. Compared with the body mass index category 25.0-29.9 kg/m, hospital mortality was higher among underweight (body mass index, < 18.5; relative risk, 1.35; 95% CI, 1.32-1.39), normal weight (body mass index, 18.5-24.9; relative risk, 1.10; 95% CI, 1.09-1.12), and the extremely obese (body mass index, ≥ 50.0; relative risk, 1.10; 95% CI, 1.05-1.15). However, the risk was not statistically different from patients with body mass index 30.0-49.9 kg/m. Among patients ordered early enteral nutrition, the risk of mortality in the body mass index category 25.0-29.9 kg/m was not statistically different from those in the normal weight or extremely obese groups. CONCLUSIONS: A survival advantage for overweight and obese patients was observed in this large cohort of critically ill patients. However, among those ordered early enteral nutrition, the survival disadvantage for body mass index categories less than 25.0 kg/m was minimal or unobservable when compared with higher body mass index categories.

B7-h1 expressed by activated CD8 T cells is essential for their survival.

An immunoinhibitory role of B7 homologue 1 (B7-H1) expressed by non-T cells has been established; however, the function of B7-H1 expressed by T cells is not clear. Peak expression of B7-H1 on Ag-primed CD8 T cells was observed during the contraction phase of an immune response. Unexpectedly, B7-H1 blockade at this stage reduced the numbers of effector CD8 T cells, suggesting B7-H1 blocking Ab may disturb an unknown function of B7-H1 expressed by CD8 T cells. To exclusively examine the role of B7-H1 expressed by T cells, we introduced B7-H1 deficiency into TCR transgenic (OT-1) mice. Naive B7-H1-deficient CD8 T cells proliferated normally following Ag stimulation; however, once activated, they underwent more robust contraction in vivo and more apoptosis in vitro. In addition, B7-H1-deficient CD8 T cells were more sensitive to Ca-dependent and Fas ligand-dependent killing by cytotoxic T lymphocytes. Activation-induced Bcl-x(L) expression was lower in activated B7-H1-deficient CD8 T cells, whereas Bcl-2 and Bim expression were comparable to the wild type. Transfer of effector B7-H1-deficient CD8 T cells failed to suppress tumor growth in vivo. Thus, upregulation of B7-H1 on primed T cells helps effector T cells survive the contraction phase and consequently generate optimal protective immunity.

TLR3-stimulated dendritic cells up-regulate B7-H1 expression and influence the magnitude of CD8 T cell responses to tumor vaccination.

Agonists of TLR have been explored as vaccine adjuvants for tumor immunotherapy. However, their immunological consequences are not fully understood. Although TLR signaling increases the functional potential of dendritic cells (DCs) for priming T cells, coinduction of potentially negative immunoregulatory capacities may impair effector T cell generation. We examined the expression and function of B7 family costimulatory molecules on DCs after activation with the TLR3 agonist, polyinosinic:polycytidylic acid. We demonstrated that polyinosinic:polycytidylic acid consistently up-regulated both B7-2 and B7-H1 molecules on resident, migratory DCs from spleen and lymph nodes. Depletion or blockade of B7-H1 on activated DCs increased the magnitude of effector CD8 T cell expansion. DC-based or protein-based tumor vaccines, in combination with B7-H1 blockade, induced strong effector CD8 T cell responses, resulting in protective immunity against newly established tumors. Our studies suggest that TLR3 signaling has the potential to up-regulate both positive and negative coregulatory molecules on APCs. Selective blockade of negative regulatory molecules in combination with TLR3 agonist may be an effective strategy for increasing the efficacy of tumor vaccines.

Chibby cooperates with 14-3-3 to regulate beta-catenin subcellular distribution and signaling activity.

beta-Catenin functions in both cell-cell adhesion and as a transcriptional coactivator in the canonical Wnt pathway. Nuclear accumulation of beta-catenin is the hallmark of active Wnt signaling and is frequently observed in human cancers. Although beta-catenin shuttles in and out of the nucleus, the molecular mechanisms underlying its translocation remain poorly understood. Chibby (Cby) is an evolutionarily conserved molecule that inhibits beta-catenin-mediated transcriptional activation. Here, we identified 14-3-3epsilon and 14-3-3zeta as Cby-binding partners using affinity purification/mass spectrometry. 14-3-3 proteins specifically recognize serine 20 within the 14-3-3-binding motif of Cby when phosphorylated by Akt kinase. Notably, 14-3-3 binding results in sequestration of Cby into the cytoplasm. Moreover, Cby and 14-3-3 form a stable tripartite complex with beta-catenin, causing beta-catenin to partition into the cytoplasm. Our results therefore suggest a novel paradigm through which Cby acts in concert with 14-3-3 proteins to facilitate nuclear export of beta-catenin, thereby antagonizing beta-catenin signaling.

Questionable relevance of gamma delta T lymphocytes in renal cell carcinoma.

Adoptive gammadelta T cell immunotherapy has moved briskly into clinical trials prompted by several small studies suggesting abundant accumulation of gammadelta T cells within renal cell carcinoma (RCC). In this study, we re-examined levels of gammadelta T cells within RCC tumors and correlated levels of these cells with pathologic features and outcome associated with this form of cancer. Tissues from 248 consecutive clear cell RCC tumors obtained from 2000 to 2003 were stained and quantified for total CD3+ and gammadelta T cells per mm2. Wilcoxon rank sum and Kruskal-Wallis tests were used to evaluate associations between T cell amounts and prognostic factors (age, gender, tumor size, stage, grade, tumor necrosis). Cox models were used to assess associations with RCC-specific death. Median numbers of total CD3+ and gammadelta T cells were 281/mm2 (interquartile range (IQR): 149-536) and 2.6/mm2 (IQR: 1.3-4.6), respectively. The median percentage of CD3+ T cells that were gammadelta T cells was 1.0% (IQR: 0.4-1.9). This low percentage of intratumoral gammadelta T cells was diluted even further with rising CD3+ T cell infiltration. Percentages of gammadelta T cells were not associated with even one single clinicopathologic feature examined. Median follow-up for this study was 3.1 years (48 patients died of RCC) and Cox analysis failed to demonstrate that gammadelta T cells (hazard ratio=1.02, p=0.25) were predictive of RCC-specific death. gammadelta T cells are rare and not recruited nor expanded within RCC tumors. Percentages of gammadelta T cells fail to correlate with any prognostic features of RCC nor specific death. As such, the role of gammadelta T cells in RCC immunobiology remains questionable.

Targeting molecular and cellular inhibitory mechanisms for improvement of antitumor memory responses reactivated by tumor cell vaccine.

Development of effective vaccination approaches to treat established tumors represents a focus of intensive research because such approaches offer the promise of enhancing immune system priming against tumor Ags via restimulation of pre-existing (memory) antitumoral helper and effector immune cells. However, inhibitory mechanisms, which function to limit the recall responses of tumor-specific immunity, remain poorly understood and interfere with therapies anticipated to induce protective immunity. The mouse renal cell carcinoma (RENCA) tumor model was used to investigate variables affecting vaccination outcomes. We demonstrate that although a whole cell irradiated tumor cell vaccine can trigger a functional antitumor memory response in the bone marrows of mice with established tumors, these responses do not culminate in the regression of established tumors. In addition, a CD103+ regulatory T (Treg) cell subset accumulates within the draining lymph nodes of tumor-bearing mice. We also show that B7-H1 (CD274, PD-L1), a negative costimulatory ligand, and CD4+ Treg cells collaborate to impair the recall responses of tumor-specific memory T cells. Specifically, mice bearing large established RENCA tumors were treated with tumor cell vaccination in combination with B7-H1 blockade and CD4+ T cell depletion (triple therapy treatment) and monitored for tumor growth and survival. Triple treatment therapy induced complete regression of large established RENCA tumors and raised long-lasting protective immunity. These results have implications for developing clinical antitumoral vaccination regimens in the setting in which tumors express elevated levels of B7-H1 in the presence of abundant Treg cells.