Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project.

BACKGROUND: Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy; however, there is empirical variability across panel assays and factors contributing to this variability have not been comprehensively investigated. Identifying sources of variability can help facilitate comparability across different panel assays, which may aid in broader adoption of panel assays and development of clinical applications. MATERIALS AND METHODS: Twenty-nine tumor samples and 10 human-derived cell lines were processed and distributed to 16 laboratories; each used their own bioinformatics pipelines to calculate TMB and compare to whole exome results. Additionally, theoretical positive percent agreement (PPA) and negative percent agreement (NPA) of TMB were estimated. The impact of filtering pathogenic and germline variants on TMB estimates was assessed. Calibration curves specific to each panel assay were developed to facilitate translation of panel TMB values to whole exome sequencing (WES) TMB values. RESULTS: Panel sizes >667 Kb are necessary to maintain adequate PPA and NPA for calling TMB high versus TMB low across the range of cut-offs used in practice. Failure to filter out pathogenic variants when estimating panel TMB resulted in overestimating TMB relative to WES for all assays. Filtering out potential germline variants at >0% population minor allele frequency resulted in the strongest correlation to WES TMB. Application of a calibration approach derived from The Cancer Genome Atlas data, tailored to each panel assay, reduced the spread of panel TMB values around the WES TMB as reflected in lower root mean squared error (RMSE) for 26/29 (90%) of the clinical samples. CONCLUSIONS: Estimation of TMB varies across different panels, with panel size, gene content, and bioinformatics pipelines contributing to empirical variability. Statistical calibration can achieve more consistent results across panels and allows for comparison of TMB values across various panel assays. To promote reproducibility and comparability across assays, a software tool was developed and made publicly available.

Near-infrared fluorescent image-guided lymph node dissection compared with locoregional lymphadenectomies in dogs with mast cell tumours.

OBJECTIVES: Near-infrared fluorescent imaging has been described for intraoperative mapping of the draining lymph nodes in human cancer and canine oral tumours. The aim of this study was to retrospectively describe the results of lymphadenectomies in dogs with mast cell tumours treated either by standard unguided locoregional lymph node dissection or near-infrared fluorescent image-guided lymph node dissection. METHODS: Medical records between 2012 and 2020 were reviewed for dogs that were presented for surgical resection of mast cell tumours with concurrent lymphadenectomy either with (near-infrared fluorescent image-guided lymph node dissection) or without near-infrared fluorescence image guidance (lymph node dissection). The number and location of lymph nodes planned for surgical dissection and actually dissected nodes, presence of metastases and perioperative complications were recorded. RESULTS: Thirty-five patients underwent near-infrared fluorescent image-guided lymph node dissection, and 43 lymph node dissections. The number of nodes preoperatively planned for resection were 70 and 68, respectively. Fifty-eight of those (83%) were identified during near-infrared fluorescent image-guided lymph node dissection procedures, compared with 50 (74%) during lymph node dissection. near-infrared fluorescent image-guided lymph node dissection resulted in resection of additional fluorescent nodes not corresponding to locoregional nodes in 15 of 35 dogs. Using near-infrared fluorescent image-guided lymph node dissection, we identified at least one metastatic node in 68% of dogs (24 of 35) compared with 33% (14 of 43) when lymph node dissection was used without imaging. No complications related to near-infrared fluorescent imaging were reported. CLINICAL SIGNIFICANCE: The present study suggests that near-infrared imaging is a promising technique for intraoperative detection of the draining lymph nodes in dogs with mast cell tumours. Further validation of the technique is required to assess if near-infrared fluorescent imaging can detect the true sentinel lymph node.

The role of sentinel lymph node mapping in small animal veterinary medicine: A comparison with current approaches in human medicine.

The relevance of regional lymph node (LN) assessment to quantify the metastatic spread of cancer is well recognized in veterinary oncology. Evaluation of LNs is critical for tumour staging. However, sampling the correct LN may not be possible without sentinel lymph node (SLN) mapping. Methods for diagnostic imaging and intraoperative detection of SLNs are well established in human medicine, in particular, the combination of lymphoscintigraphy and intraoperative application of blue dyes. Nevertheless, alternative imaging techniques are available and have gained increasing interest. Successful implementation of these techniques in dogs have been reported in both clinical and experimental studies. This review aims to provide an overview of SLN mapping techniques in human and veterinary medicine.

Cardiovascular and pupillary autonomic nervous dysfunction in patients with rheumatoid arthritis - a cross-sectional and longitudinal study.

OBJECTIVES: Patients with inflammatory diseases often demonstrate autonomic nervous dysfunction. This study was initiated to investigate cardiovascular (CAD) or pupillary autonomic dysfunction (PAD) in patients with rheumatoid arthritis (RA). METHODS: Between 1997 and 1998, 33 RA patients were examined for characteristics, and parameters of CAD and PAD. In a longitudinal part of this study, thirty patients have been re-evaluated 8.3 +/- 0.1 yr later (response rate = 91%). RESULTS: A total of 18 patients (60%) demonstrated either CAD or PAD. The prevalence of CAD was 6/30 (20%) and the prevalence of PAD was 15/30 (50%). Of all cardiovascular tests, the Ewing test demonstrated the worst results (13/30 patients were below the 5th percentile). Similar as in other diseases, several RA patients demonstrated autonomic nervous hyperreflexia with values above the 95 th percentile (relative variation coefficient: 7/30; respiratory sinus arrhythmia measure: 12/30; Valsalva measure: 1/30; Ewing measure: 0/30; latency time of pupillary light reflex: 5/30; maximal pupillary area: 0/30). During the 8-year observation period, 4/30 RA patients died. Non-survivors as compared to survivors had increased heart rate variation in the respiratory arrhythmia test (p= 0.038, hyperreflexia) but largely decreased heart rate variation in the Ewing test (p= 0.009, hyporeflexia). Non-survivors as compared to survivors demonstrated more frequent pupillary autonomic dysfunction (100% vs. 42%, p= 0.035). CONCLUSION: This study demonstrates that CAD and PAD were frequent in patients with RA. Patients with a poor test result in the Ewing test and PAD might have an increased risk of death. This study in RA patients demonstrates similar results as in patients with diabetes mellitus.

Molecular recognition of anions by synthetic receptors.

Over the past year, several significant developments have been made in the field of anion binding. The fundamental principles of molecular recognition are increasingly being better understood, and of particular interest are reports of several synthetic anion receptors able to perform their task in complex natural media. Additionally, macroscopic devices such as anion specific electrodes and membranes based on a molecular recognition approach are now being made.

Persistent STAT5 activation in myeloid neoplasms recruits p53 into gene regulation.

STAT (Signal Transducer and Activator of Transcription) transcription factors are constitutively activated in most hematopoietic cancers. We previously identified a target gene, LPP/miR-28 (LIM domain containing preferred translocation partner in lipoma), induced by constitutive activation of STAT5, but not by transient cytokine-activated STAT5. miR-28 exerts negative effects on thrombopoietin receptor signaling and platelet formation. Here, we demonstrate that, in transformed hematopoietic cells, STAT5 and p53 must be synergistically bound to chromatin for induction of LPP/miR-28 transcription. Genome-wide association studies show that both STAT5 and p53 are co-localized on the chromatin at 463 genomic positions in proximal promoters. Chromatin binding of p53 is dependent on persistent STAT5 activation at these proximal promoters. The transcriptional activity of selected promoters bound by STAT5 and p53 was significantly changed upon STAT5 or p53 inhibition. Abnormal expression of several STAT5-p53 target genes (LEP, ATP5J, GTF2A2, VEGFC, NPY1R and NPY5R) is frequently detected in platelets of myeloproliferative neoplasm (MPN) patients, but not in platelets from healthy controls. In conclusion, persistently active STAT5 can recruit normal p53, like in the case of MPN cells, but also p53 mutants, such as p53 M133K in human erythroleukemia cells, leading to pathologic gene expression that differs from canonical STAT5 or p53 transcriptional programs.

Special pacemaker catheter techniques. The transmediastinal placement of sensing electrodes.

The clinical utilization of atrial programmed pacemakers is limited by the lead systems available for sensing of atrial activity. The endocardial method of lead placement is burdened by a dislodgement rate of up to 30 per cent. Alternatively, the patient must submit to the risks of a thoracotomy. Thirty-one patients have been treated with a transmediastinally, retrocardially positioned atrial detector electrode. In 20 patients (65 per cent) the detector performed as desired with no postimplant revision. In 11 patients (35 per cent) corrective measures were required primarily to correct lead placement; seven of these were corrected under local anesthesia merely by pulling the catheter. Spontaneous lead dislocation occurred in four patients. Four patients (13 per cent) underwent remediastinoscopy due to cranial displacement of the detector electrode with a resulting decrease in atrial potential to less than 0.5 mV. For technical reasons, the lead placements were performed without the benefit of x-ray illumination, with only an ECG check of the posterior atrial wall, and this may account for the relatively high incidence of revision. Transmediastinal placement of sensing electrodes presents a practicable alternative to methods presently used.

A killing disease epidemic among displaced Sudanese population identified as visceral leishmaniasis.

A fatal disease epidemic affected the Bentiu area in southern Sudan and led to a mass migration of the Nuer tribe searching for treatment. The initially available information revealed a high mortality rate due to a possible occurrence of tuberculosis, malaria, enteric fever or visceral leishmaniasis (VL). Serological screening of 53 of the most severely affected patients in an enzyme-linked immunosorbent assay (ELISA) or an improved direct agglutination test (DAT) revealed positivity for VL. In 39 of those patients, diagnosis was confirmed by identification of Leishmania donovani amastigotes in lymph node or bone-marrow aspirates. In a total of 2714 patients observed, 1195 (44.0%) had clinical symptoms suggesting VL: DAT positive titers (1:3200-greater than or equal to 1:12800) were obtained in 654 (24.1%), of whom 325 were confirmed parasitologically. Forty-two VL cases died before or during treatment, giving a mortality rate of 6.4%. Among the intercurrent infections diagnosed in the VL population (654), respiratory involvements (31.7%) and malaria (10.7%) were most prevalent. With the exception of four (0.6%), all other VL patients (509) responded readily to sodium stibogluconate. The factors initiating the outbreak are discussed. Malnutrition and nomadic movements to potential VL endemic areas appeared to be the most important. HIV infection as a possible predisposition seemed remote considering the clinical and epidemiological similarity to VL occurring in East Africa, adequate humoral response in DAT, and immediate positive response to specific anti-Leishmania chemotherapy.

The binding of difunctional neutral guest molecules by novel bis(tripyrrolyl) cryptands.

Bis(tripyrrolyl) cryptands are prepared via a [2 + 3] Schiff base condensation of formyltripyrrolyls with diamines; an ethyl-spaced hexapyrrole cryptand is shown to bind strongly ethane-1,2-diamine and ethane-1,2-diol in chloroform solution.

Spontaneous regression and successful laser prophylaxis in progressive outer retinal necrosis syndrome.

PURPOSE: To describe a case of progressive outer retinal necrosis syndrome that regressed spontaneously after discontinuation of all systemic antiviral medications with macular sparing after prophylactic laser photocoagulation of the posterior pole. METHODS: Prophylactic laser photocoagulation surrounding the posterior pole was performed in an attempt to spare the macula from detachment in a patient with progressive outer retinal necrosis. RESULTS: Progressive outer retinal necrosis regressed spontaneously without systemic antiviral medications. The posterior pole within the area of photocoagulation remained attached. CONCLUSIONS: Prophylactic laser treatment surrounding the posterior pole rather than peripheral retina may allow more time for formation of firm chorioretinal adhesions and protect the macula from detachment.

Cenani-Lenz syndrome in father and daughter.

We present a father and daughter with typical clinical and radiological features of Cenani-Lenz syndrome. Cenani-Lenz syndrome has been delineated as a type of complete syndactyly resembling the spoon hand seen in Apert syndrome, with as important additional feature, the fusion of metacarpals and disorganization of the phalanges. Based on the observation of the syndrome in at least two affected siblings born to normal parents and the consanguinity in one family autosomal recessive inheritance was proposed. The findings in the present family could indicate that Cenani-Lenz syndrome may be genetically heterogeneous. Another possible explanation could be that the occurrence in affected siblings born to normal parents could be explained by gonadal mosaicism for an autosomal dominant gene.

[Distal hyperirrigation syndrome. Clinical and physiopathological aspects]. / Le syndrome d'hyperirrigation distale. Clinique et physiopathologie.

In this retrospective study, distal hyperirrigation syndrome was identified by "irrigraphy", a functional exploration method used to define an irrigation index at various levels of the lower limbs as determined by pulse wave amplitude, heart rare and segmental resistances. In 47 lower limbs studied, there were 26 unequivocal, 14 relative and 7 "masked" hyperirrigations. The main etiology was diabetes (24 limbs), but the syndrome was also noted in cases of peripheral neuropathy and chronic venous insufficiency. There was no basic difference between unequivocal and relative hyperirrigations. Some hyperirrigation states were not apparent in irrigraphy because of arterial lesions on upstream axes. The syndrome was also observed in approximately the same number of cases in insulin-dependent and noninsulin-dependent diabetes. The clinical disorders observed were especially peripheral trophic ones, notably perforating ulcers of the foot or various ulcers. Changes in the irrigraphic profile were followed regularly in 20 limbs. The rise in distal irrigation indices was due to a drop in peripheral resistances related to an abnormal opening up of arteriovenous anastomoses. A state of spontaneous sympathectomy was thus constituted, particularly in diabetic patients. The process was similar in syndromes of neurologic origin and in venous stasis. The mechanism was local, with venous hypertension causing the opening up of arteriovenous shunts. However, microangiopathic lesions must also be taken into account, since they can cause or favor arteriovenous shunting. The opening up of arteriovenous anastomoses is in effect the element common to all syndromes of distal hyperirrigation of various origins.(ABSTRACT TRUNCATED AT 250 WORDS)

[Maternal pulmonary edema as an anesthesia complication after intravenous tocolysis and stimulating of lung maturation]. / Mütterliches Lungenödem als Narkosekomplikation bei Status nach intravenöser Tokolyse und Lungenreifungsstimulation.

Maternal lung edema due to the use of beta-mimetic tocolytic agents is a well-documented complication. The risk increases if several other factors are present: infectious diseases, the use of inhaled anesthetics, EPH gestosis, hydramnios, twin gestation and preexisting cardiovascular disease. The complications induced by beta-mimetic tocolytic agents can be reduced by remembering their side effects and contraindications and restricting fluid intake. During obstetric general anesthesia in patients undergoing tocolysis, the infusion of large amounts of saline, as is widely practised today, is strictly contraindicated.

[Changes in indications for obstetric peridural anesthesia in our clinic]. / Wandel in der Indikationsstellung zur geburtshilflichen Periduralanästhesie an unserer Klinik.

In relation to the Swiss average our hospital has had a constant high rate of spontaneous deliveries and a low rate of cesarean sections. On the other hand the rate of obstetrical peridural anesthesia has been increasing significantly since 1986. This is above all related to its more frequent usage in cases of cervical dystocia and intolerable birth pain. Exactly in these indications peridural anesthesia has been very successful. In almost three quarters of the above-mentioned cases a cesarean section can be avoided due to peridural anesthesia.

[Acute pseudo-obstruction of the colon (Ogilvie syndrome) after Cesarean section]. / Akute Pseudoobstruktion des Kolons (Ogilvie-Syndrom) nach Sectio caesarea.

In a 27-year-old woman a spontaneous perforation of the bowel developed after cesarean section. The clinical picture, pathophysiological aspects and prophylactic treatment of Ogilvie's syndrome are discussed. This rare but serious complication could have been avoided if the clinical picture and its simple conservative treatment had been known.

Ex vivo expansion of normal and chronic myeloid leukemic stem cells without functional alteration using a NUP98HOXA10homeodomain fusion gene.

HOX genes have been implicated as regulators of normal and leukemic stem cell functionality, but the extent to which these activities are linked is poorly understood. Previous studies revealed that transduction of primitive mouse hematopoietic cells with a NUP98HOXA10homeodomain (NA10HD) fusion gene enables a subsequent rapid and marked expansion in vitro of hematopoietic stem cell numbers without causing their transformation or deregulated expansion in vivo. To determine whether forced expression of NA10HD in primitive human cells would have a similar effect, we compared the number of long-term culture-initiating cells (LTC-ICs) present in cultures of lenti-NA10HD versus control virus-transduced CD34(+) cells originally isolated from human cord blood and chronic phase (CP) chronic myeloid leukemia (CML) patients. We found that NA10HD greatly increases outputs of both normal and Ph(+)/BCR-ABL(+) LTC-ICs, and this effect is particularly pronounced in cultures containing growth factor-producing feeders. Interestingly, NA10HD did not affect the initial cell cycle kinetics of the transduced cells nor their subsequent differentiation. Moreover, immunodeficient mice repopulated with NA10HD-transduced CP-CML cells for more than 8 months showed no evidence of altered behavior. Thus, NA10HD provides a novel tool to enhance both normal and CP-CML stem cell expansion in vitro, without apparently altering other properties.

Genetic variations in androgen metabolism genes and associations with prostate cancer in South African men.

Background. In South Africa white men have the highest incidence of prostate cancer (PCa), coloured (mixed ancestry) men have an intermediate incidence, and low incidences are reported for black and Asian men. It has been suggested that ethnic differences in incidence and mortality of PCa are related to genetic variations in genes that regulate androgen metabolism. We investigated the role of genetic variants in the androgen metabolism genes and the probability of developing PCa in South African coloured and white men. Methods. Genotype and allele counts and frequencies of single nucleotide polymorphisms (SNPs) in CYP3A5, CYP3A4 and CYP3A43 were assessed in coloured men (160 case individuals, 146 control individuals) and white men (121 case individuals, 141 control individuals). Results. A genetic association indicating an increased probability of developing PCa was observed with the G allele of the SNP rs2740574 in CYP3A4 in coloured men, the A allele of rs776746 (CYP3A5) and the G allele of rs2740574 (CYP3A4) in white men, and the G allele of rs2740574 and the C allele of rs501275 (CYP3A43) in the combined ethnic groups analysis. In addition, we identified allele combinations (termed haplotypes) with significantly higher frequencies in the PCa case individuals than in the control individuals. Conclusions. The findings support the role of variants in genes that regulate androgen metabolism and the probability of developing PCa. The study paves the way to identify other genetic associations in South African men, and to establish genetic profiles that could be used to determine disease progression and prognosis.