POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies

Heterozygous pathogenic variants in POLR1A, which encodes the largest subunit of RNA Polymerase I, were previously identified as the cause of acrofacial dysostosis, Cincinnati-type. The predominant phenotypes observed in the cohort of 3 individuals were craniofacial anomalies reminiscent of Treacher Collins syndrome. We subsequently identified 17 additional individuals with 12 unique heterozygous variants in POLR1A and observed numerous additional phenotypes including neurodevelopmental abnormalities and structural cardiac defects, in combination with highly prevalent craniofacial anomalies and variable limb defects. To understand the pathogenesis of this pleiotropy, we modeled an allelic series of POLR1A variants in vitro and in vivo. In vitro assessments demonstrate variable effects of individual pathogenic variants on ribosomal RNA synthesis and nucleolar morphology, which supports the possibility of variant-specific phenotypic effects in affected individuals. To further explore variant-specific effects in vivo, we used CRISPR-Cas9 gene editing to recapitulate two human variants in mice. Additionally, spatiotemporal requirements for Polr1a in developmental lineages contributing to congenital anomalies in affected individuals were examined via conditional mutagenesis in neural crest cells (face and heart), the second heart field (cardiac outflow tract and right ventricle), and forebrain precursors in mice. Consistent with its ubiquitous role in the essential function of ribosome biogenesis, we observed that loss of Polr1a in any of these lineages causes cell-autonomous apoptosis resulting in embryonic malformations. Altogether, our work greatly expands the phenotype of human POLR1A-related disorders and demonstrates variant-specific effects that provide insights into the underlying pathogenesis of ribosomopathies.

Insurance denials and diagnostic rates in a pediatric genomic research cohort

PURPOSE

This study aimed to assess the amount and types of clinical genetic testing denied by insurance and the rate of diagnostic and candidate genetic findings identified through research in patients who faced insurance denials.

METHODS

Analysis consisted of review of insurance denials in 801 patients enrolled in a pediatric genomic research repository with either no previous genetic testing or previous negative genetic testing result identified through cross-referencing with insurance prior-authorizations in patient medical records. Patients and denials were also categorized by type of insurance coverage. Diagnostic findings and candidate genetic findings in these groups were determined through review of our internal variant database and patient charts.

RESULTS

Of the 801 patients analyzed, 147 had insurance prior-authorization denials on record (18.3%). Exome sequencing and microarray were the most frequently denied genetic tests. Private insurance was significantly more likely to deny testing than public insurance (odds ratio = 2.03 [95% CI = 1.38-2.99] P = .0003). Of the 147 patients with insurance denials, 53.7% had at least 1 diagnostic or candidate finding and 10.9% specifically had a clinically diagnostic finding. Fifty percent of patients with clinically diagnostic results had immediate medical management changes (5.4% of all patients experiencing denials).

CONCLUSION

Many patients face a major barrier to genetic testing in the form of lack of insurance coverage. A number of these patients have clinically diagnostic findings with medical management implications that would not have been identified without access to research testing. These findings support re-evaluation of insurance carriers' coverage policies.

Novel blended SNRPE-related spliceosomopathy phenotype characterized by microcephaly and congenital atrichia

Variants in genes encoding core components of the spliceosomes are associated with craniofacial syndromes, collectively called craniofacial spliceosomopathies. SNRPE encodes a core component of pre-mRNA processing U-rich small nuclear ribonuclear proteins (UsnRNPs). Heterozygous variants in SNRPE have been reported in six families with isolated hypotrichosis simplex in addition to one case of isolated non syndromic congenital microcephaly. Here, we report a patient with a novel blended phenotype of microcephaly and congenital atrichia with multiple congenital anomalies due to a de novo intronic SNRPE deletion, c.82-28_82-16del, which results in exon skipping. As discussed within, this phenotype, which we propose be named SNRPE-related syndromic microcephaly and hypotrichosis, overlaps other craniofacial splicesosomopathies.

An effective sub-quadratic scaling atomic-orbital reformulation of the scaled opposite-spin RI-CC2 ground-state model using Cholesky-decomposed densities and an attenuated Coulomb metric

An atomic-orbital reformulation of the Laplace-transformed scaled opposite-spin (SOS) coupled cluster singles and doubles (CC2) model within the resolution of the identity (RI) approximation (SOS-RI-CC2) is presented that extends its applicability to molecules with several hundreds of atoms and triple-zeta basis sets. We exploit sparse linear algebra and an attenuated Coulomb metric to decrease the disk space demands and the computational efforts. In this way, an effective sub-quadratic computational scaling is achieved with our ω-SOS-CDD-RI-CC2 model. Moreover, Cholesky decomposition of the ground-state one-electron density matrix reduces the prefactor, allowing for an early crossover with the molecular orbital formulation. The accuracy and performance of the presented method are investigated for various molecular systems.

Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes

PURPOSE

This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program.

METHODS

Extensive analyses of 960 families with suspected genetic disorders included short-read exome sequencing and short-read genome sequencing (srGS); PacBio HiFi long-read genome sequencing (HiFi-GS); variant calling for single nucleotide variants (SNV), structural variant (SV), and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants, and pedigrees were stored in PhenoTips database, with data sharing through controlled access the database of Genotypes and Phenotypes.

RESULTS

Diagnostic rates ranged from 11% in patients with prior negative genetic testing to 34.5% in naive patients. Incorporating SVs from genome sequencing added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs compared with srGS. Variants and genes of unknown significance remain the most common finding (58% of nondiagnostic cases).

CONCLUSION

Computational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated using HiFi-GS sequencing. Importantly, community research is supported by sharing real-time data to accelerate gene validation and by providing HiFi variant (SNV/SV) resources from >1000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses.

[Update of the S2k guidelines : Surgical treatment of benign thyroid diseases]

Thyroid resections represent one of the most common operations with 76,140 interventions in the year 2016 in Germany (source Destatis). These are predominantly benign thyroid gland diseases. Recommendations for the operative treatment of benign thyroid diseases were last published by the CAEK in 2010 as S2k guidelines (Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften e.V. [AWMF] 003/002) against the background of increasingly more radical resection procedures. Hemithyroidectomy and thyroidectomy are routinely performed for benign thyroid disease in practice. The operation-specific risks show a clear increase with the extent of the resection. Therefore, weighing-up of the risk-indications ratio between unilateral lobectomy or thyroidectomy necessitates an independent evaluation of the indications for both sides. This principle in particular has been used to update the guidelines. In addition, the previously published recommendations of the CAEK for correct execution and consequences of intraoperative neuromonitoring were included into the guidelines, which in particular serve the aim to avoid bilateral recurrent laryngeal nerve paralysis. Moreover, the recommendations for the treatment of postoperative complications, such as hypoparathyroidism and postoperative infections were revised. The updated guidelines therefore represent the current state of the science as well as the resulting surgical practice.

Stationäre und ambulante Thromboembolieprophylaxe in der Chirurgie und der perioperativen Medizin

Präambel: Alle aufgeführten medizinischen Fachgesellschaften haben sich zusammengefunden, um die früheren verschiedenen Empfehlungen zur Thromboembolieprophylaxe zu aktualisieren und in einer gemeinsamen »Leitlinie zur stationären und ambulanten Thromboembolieprophylaxe in der perioperativen Medizin« zusammenzufassen. Dazu wurden in einem ersten Schritt durch eine Konsensuskonferenz mit nominalem Gruppenprozess die früheren Empfehlungen (Fassung vom Juni 2000) überarbeitet (S2-Leitlinie). Dies erschien notwendig, um neue Therapieprinzipien und neu zugelassene Medikamente zu berücksichtigen. Als nächster Schritt erfolgt die Weiterentwicklung der vorliegenden Leitlinie nach der Vorgaben der 3. Stufe der Leitlinienentwicklung der AWMF (S3-Leitlinie).

Der präoperative Gerinnungsstatus

Der Wert einer präoperativen gerinnungsanalytischen Screening-Untersuchung zur Erhöhung der Patientensicherheit wird kontrovers diskutiert. In einer prospektiven Beobachtungsstudie mit dem Endpunkt Blutungskomplikation wurde bei 638 Patienten aus der elektiven Viszeralchirurgie die Bedeutung der präoperativen Bestimmung von Quick-Wert, APTT und Thrombozytenzahl untersucht. Zusätzlich wurde bei allen Patienten eine standardisierte Anamnese bezüglich einer möglichen Hämostasestörung erhoben. Postoperative Blutungskomplikationen wurden bei 3,1% der Patienten beobachtet. Die Gerinnungsanalytik zeigte bei 5,8% der Patienten Auffälligkeiten. Die Inzidenz von Blutungskomplikationen bei Patienten mit normaler bzw. auffälliger Gerinnungsuntersuchung unterschied sich nicht (p = 0,4141). Da sich 90% der Blutungskomplikationen bei Patienten mit normalem Gerinnungsstatus ereigneten, war die Sensitivität der Gerinnungsanalytik für das Auftreten einer Blutungskomplikation mit 10% ausgesprochen gering. Durch die standardisierte Anamnese und eine sich daran anschließende Spezialdiagnostik wurden 3 Patienten mit einem v.-Willebrand-Typ I identifiziert. Bei diesen Patienten war der Gerinnungsstatus normal.

Further clinical and molecular delineation of the 15q24 microdeletion syndrome

Background

Chromosome 15q24 microdeletion syndrome is a rare genomic disorder characterised by intellectual disability, growth retardation, unusual facial morphology and other anomalies. To date, 20 patients have been reported; 18 have had detailed breakpoint analysis.

Aim

To further delineate the features of the 15q24 microdeletion syndrome, the clinical and molecular characterisation of fifteen patients with deletions in the 15q24 region was performed, nearly doubling the number of reported patients.

Methods

Breakpoints were characterised using a custom, high-density array comparative hybridisation platform, and detailed phenotype information was collected for each patient.

Results

Nine distinct deletions with different breakpoints ranging in size from 266 kb to 3.75 Mb were identified. The majority of breakpoints lie within segmental duplication (SD) blocks. Low sequence identity and large intervals of unique sequence between SD blocks likely contribute to the rarity of 15q24 deletions, which occur 8–10 times less frequently than 1q21 or 15q13 microdeletions in our series. Two small, atypical deletions were identified within the region that help delineate the critical region for the core phenotype in the 15q24 microdeletion syndrome.

Conclusion

The molecular characterisation of these patients suggests that the core cognitive features of the 15q24 microdeletion syndrome, including developmental delays and severe speech problems, are largely due to deletion of genes in a 1.1–Mb critical region. However, genes just distal to the critical region also play an important role in cognition and in the development of characteristic facial features associated with 15q24 deletions. Clearly, deletions in the 15q24 region are variable in size and extent. Knowledge of the breakpoints and size of deletion combined with the natural history and medical problems of our patients provide insights that will inform management guidelines. Based on common phenotypic features, all patients with 15q24 microdeletions should receive a thorough neurodevelopmental evaluation, physical, occupational and speech therapies, and regular audiologic and ophthalmologic screening.

A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay

We report the identification of a recurrent 520-kbp 16p12.1 microdeletion significantly associated with childhood developmental delay. The microdeletion was detected in 20/11,873 cases vs. 2/8,540 controls (p=0.0009, OR=7.2) and replicated in a second series of 22/9,254 cases vs. 6/6,299 controls (p=0.028, OR=2.5). Most deletions were inherited with carrier parents likely to manifest neuropsychiatric phenotypes (p=0.037, OR=6). Probands were more likely to carry an additional large CNV when compared to matched controls (10/42 cases, p=5.7×10^-5, OR=6.65). Clinical features of cases with two mutations were distinct from and/or more severe than clinical features of patients carrying only the co-occurring mutation. Our data suggest a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity suggests that this two-hit model may be more generally applicable to neuropsychiatric disease.

Symptom reporting in cancer patients II: relations to social desirability, negative affect, and self-reported health behaviors

BACKGROUND

Patients' appraisal of somatic symptoms is correlated with their negative affect. The authors have investigated whether social desirability is associated with patients' symptom and health behavior reporting.

METHODS

One hundred fourteen surgical cancer patients who participated in either an outpatient or an inpatient follow-up care program filled out the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-C30, the New Social Desirability Scale, and a health behavior checklist.

RESULTS

Patients' reports of somatic symptoms were correlated inversely with social desirability (r = -0.50) and positively with negative affect (r = 0.72). When objective health and demographic variables (e.g., prognosis, adjuvant therapy prior to follow-up, and gender) were entered first in hierarchical multiple regression analyses, social desirability and negative affect accounted for an additional 16% and 36% of the symptom variance, respectively. Similar results were found when global quality of life was the dependent variable. Self-reported health behaviors were explained only through the set of health and demographic variables (14%), and social desirability and negative affect did not account for additional variance. On the average, patients reported that they had a median of 4.7 (out of a list of 21) self-initiated health behaviors, and 11% of the patients admitted to having used unproven therapies.

CONCLUSIONS

Symptom reports do not give a pure picture of patients' health status, but they are strongly correlated with social desirability and negative affect. Detection of such psychologic variables is essential to understanding the dynamics of quality of life. In applied settings, quality-of-life measures should be used together with conventional criteria. As practical experience and scientific understanding grow, the relative positioning of these patient-oriented versus clinic-oriented endpoints will become clear.

[Malignant non-epithelial tumors of the pancreas]

Nonepithelial malignant tumors of the pancreas are extremely rare neoplasms with a frequency of approximately 0.6%. They are always explored because of a suspected diagnosis of pancreatic carcinoma. Amongst the more than 600 primary pancreatic neoplasms in our pancreatic tumor archive only 5 neoplasms were of nonepithelial origin (one was a malignant peripheral nerve sheath tumor [MPNST], one a leiomyosarcoma, one a malignant mesothelioma, and two were peripheral neuroectodermal tumors [PNET]. The differential diagnosis includes secondary infiltration of the pancreas by mesenchymal tumors of the retroperitoneum, undifferentiated pancreatic carcinoma and, especially in the case of PNET, malignant lymphoma. Preoperative chemotherapy and down-staging can improve the operability and prognosis, especially in PNET.

[Radiological thorax monitoring in ventilated intensive-care patients]

PURPOSE

At many institutions chest x-rays (CXR) are routinely performed on mechanically ventilated patients on a daily basis. Among the aims of this study was the assessment of a) frequency of clinically relevant findings from routine CXR in surgical patients under mechanical ventilation, b) comparison of expectations of clinically important CXR findings with estimation of clinical relevance of findings once films were obtained, c) indications and clinical consequences of findings from CXR requested in addition to routine films.

METHODS

Prospective study, 40 patients with 741 CXR. Standardised film reporting. Daily recording of clinical data by means of an evaluation score. Interview of intensive-care physicians for assessment of: what information was expected from any routine CXR? did CXR offer helpful information for further treatment planning?

RESULTS

26% of routine CXR had a considerable therapeutical impact. 43% of all routine CXR were expected to have an influence on patient management, 57% were not. 16% of those CXR that had been expected not to offer essential information, disclosed relevant findings. Of the additionally obtained CXR, 53% were performed to check position of endotracheal tube and catheters and 47% related to other indications.

CONCLUSION

Critically ill surgical patients under mechanical ventilation should have daily CXR follow-up, as one-fourth of these films has an impact on the patient's management.

[Anticoagulation after vascular surgery interventions]

Questionnaires regarding postoperative antiplatelet and anticoagulant therapy were answered by personal interviews with 35 German vascular surgeons. A 3/4 majority follow the recommendations of literature by anticoagulation after embolectomy in patients with persistent atrial fibrillation. Antiplatelet therapy is common in patients after thrombendarteriectomy and justified by improving the natural history of atherosclerotic disease. Considerable differences exist in postoperative therapy following peripheral bypass surgery. Controlled clinical trials are rare and present contradicting results. Prospective randomized multicenter studies are necessary.

[Blood-saving surgery]

Trauma, blood loss and autologous blood transfusions induce a variety of changes in the reactivity of patients' immune systems. In clinical studies the differentiation of these effects is difficult. Association between autologous blood transfusion and postoperative infection is highly likely. In surgical oncology blood transfusions are associated with poor prognosis, but probably this is more because of the circumstances that necessitate them.

[Measuring quality of life in after-care of tumor surgery. Methods, problems and applications]

The present paper deals with the feasibility and applications of quality of life measurement in the routine of a tumor follow-up clinic. 61 patients filled out the EORTC-30 questionnaire plus additional scales. Filling out the questionnaire constituted no burden for patients. Patients' responses were computed in a way as to allow for graphically presenting individual QL-profiles, as well as to compare different groups of patients. Considerations concerning the role of QL-measurement in clinical practice, in medical decision making, and in future research endeavours were brought forward.

[Daily "routine chest x-ray" in ventilated surgical intensive care patients]

We investigated the relevance of daily routine chest x-ray in intensive care for therapeutical decision. A special emphasis was put on clinical laboratory parameters according to the APACHE-II-score. Within a prospective study we investigated 40 intubated patients of our surgical intensive care unit with a total of 609 x-ray films. 26% of all pictures gained influence on therapeutical procedure. Analysis of different patient subgroups showed only between those under 50 and those above 70 years of age an important discrepancy quote of relevant films (19 vs. 31%).

[Manifestations of ruptured liver hematoma as a severe complication of HELLP syndrome]

A case of a ruptured haematoma of the liver with intra-abdominal bleeding is reported. The 26-year old primigravida was admitted in the 31st week of gestation because of a HELLP syndrome. She presented additional symptoms, that are considered typical for a HELLP syndrome, complicated by a ruptured haematoma of the liver: severe right upper-quadrant pain, decrease of haemoglobin content, enlarged liver with structural irregularities and free fluid in the abdominal cavity as examined by sonography. During Caesarean section, a subcapsular haematoma of the liver, combined with a 5 cm laceration of the organ surface, was found. The defect was closed with collagen gauze and clotted with fibrin. Additionally the liver was compressed by abdominal compression towels, which were removed 2 days later. The postoperative development was, in the main, complication free.

[Unusual dilatation of the colon in idiopathic megacolon in adulthood]

This is a report on a 20-year old patient who had been suffering from chronic constipation from her childhood. After radiography of the colon in double contrast in December 1986 the patient was admitted to hospital under suspicion of a perforation of the colon. The radiographic demonstration of the abdomen showed an exceptional dilatation of some segments of the colon but without any signs of perforation by free intraperitoneal gas. Subsequent examination led to the diagnosis of an idiopathic megacolon whereas a congenital as well as symptomatic and toxic megacolon could be excluded.

[Prevention of thromboembolism with low-dose heparin]

With an amidolytic assay plasma heparin activity is measured in patients undergoing elective abdominal surgery and general surgery under LDH-prophylaxis. The data obtained suggest that the response of the hemostatic system to 3 X 5000 U. heparin is individual and unpredictable. In 82 patients undergoing hip fracture surgery it could be demonstrated that there is a correlation between anticoagulant heparin activity and the incidence of DVT.

[Perioperative plasma antithrombin activity with "low-dose" heparin prophylaxis. Perioperatively acquired antithrombin III deficiency as a cause for the failure of heparin prophylaxis?]

Antithrombin III activity was estimated using a chromogenic substrate perioperatively in the plasma of 200 patients undergoing major elective abdominal surgery during low-dose heparin prophylaxis. With an initial value of 10.9 +/- 2 IU/ml there was a mean postoperative lowering of plasma antithrombin activity in all patients with a minimum on the second postoperative day. In patients with empirically established increased risk of thromboembolism the postoperative depression of antithrombin was significantly more pronounced (P less than 0.01) than in the control groups. An increased risk prevailed particularly in patients with malignant diseases and in major surgery, i.e. of prolonged duration. In such cases with increased risk of thromboembolism routine assessment of antithrombin III is recommended.