Abstract
Background
Monogenic autoinflammatory diseases are caused by pathogenic variants in genes that regulate innate immune responses, and are characterized by sterile systemic inflammatory ...episodes. Since symptoms can overlap within this rapidly expanding disease category, accurate genetic diagnosis is of the utmost importance to initiate early inflammation-targeted treatment and prevent clinically significant or life-threatening complications. Initial recommendations for the genetic diagnosis of autoinflammatory diseases were limited to a gene-by-gene diagnosis strategy based on the Sanger method, and restricted to the 4 prototypic recurrent fevers (MEFV, MVK, TNFRSF1A, and NLRP3 genes). The development of best practices guidelines integrating critical recent discoveries has become essential.
Methods
The preparatory steps included 2 online surveys and pathogenicity annotation of newly recommended genes. The current guidelines were drafted by European Molecular Genetics Quality Network members, then discussed by a panel of experts of the International Society for Systemic Autoinflammatory Diseases during a consensus meeting.
Results
In these guidelines, we combine the diagnostic strength of next-generation sequencing and recommendations to 4 more recently identified genes (ADA2, NOD2, PSTPIP1, and TNFAIP3), nonclassical pathogenic genetic alterations, and atypical phenotypes. We present a referral-based decision tree for test scope and method (Sanger versus next-generation sequencing) and recommend on complementary explorations for mosaicism, copy-number variants, and gene dose. A genotype table based on the 5-category variant pathogenicity classification provides the clinical significance of prototypic genotypes per gene and disease.
Conclusions
These guidelines will orient and assist geneticists and health practitioners in providing up-to-date and appropriate diagnosis to their patients.
ABSTRACT
The Human Genome Variation Society (HGVS) recommendations provide standardized nomenclature for reporting variants. This should be encouraged in molecular pathology—both for issuing ...diagnostic reports and for correct data recording in electronic databases. Many providers of external quality assessment (EQA) promote the correct use of HGVS nomenclature by scoring variant descriptions used in EQA reports. This study focuses on the type and impact of variant nomenclature errors. An assessment was made of EGFR gene variant nomenclature by four EQA providers (European Society of Pathology ESP, European Molecular Genetics Quality Network EMQN, United Kingdom National External Quality Assessment Service for Molecular Genetics, and the French national Gen&Tiss EQA scheme) for two EQA distributions. Laboratories testing for oncology biomarkers make different errors when describing EGFR gene variants. Significant differences were observed regarding inclusion of the correct reference sequence: EMQN participants made fewer errors compared to ESP EQA participants (P‐value = 0.015). The analysis of ESP EQA participants showed significant improvement over 2 years (P‐value = 0.016). Results demonstrate the need for improvement of variant reporting according to HGVS guidelines. Consequences of using incorrect mutation nomenclature are currently perceived as low by many laboratories, but the impact will rise with an increased reliance on databases to assist in result analysis.
Tumor mutational burden (TMB) has recently been approved as an agnostic biomarker for immune checkpoint inhibitors. However, methods for TMB testing have not yet been standardized. The International ...Quality Network for Pathology (IQNPath) organized a pilot external quality assessment (EQA) scheme for TMB testing. The aim of this program was the validation of the materials and the procedures for the EQA of this complex biomarker. Five formalin-fixed paraffin-embedded (FFPE) cell lines were selected to mimic the various TMB values observed in clinical practice. The FFPE samples were tested with the FoundationOne CDx (F1CDx) assay as the reference test and three commercially available targeted sequencing panels. Following this internal validation, the five cell lines were sent to 29 laboratories selected on the basis of a previous survey. Nineteen of the 23 laboratories that submitted results (82.6%) used targeted sequencing for TMB estimation. Only two laboratories performed whole exome sequencing (WES) and two assessed TMB by clinical exome. A high variability in the reported TMB values was observed. The variability was higher for samples with the highest TMB value according to the F1CDx test. However, good reproducibility of the TMB score was shown by laboratories using the same panel. The majority of laboratories did not indicate a TMB cut-off value for clinical interpretation. In conclusion, this pilot EQA scheme suggests that it is feasible to run such an EQA program for TMB assessment. However, the results of our pilot highlight the numerous challenges for the standardization of this test.
Hereditary Breast and Ovarian Cancer (HBOC) is a genetic condition associated with increased risk of cancers. The past decade has brought about significant changes to hereditary breast and ovarian ...cancer (HBOC) diagnostic testing with new treatments, testing methods and strategies, and evolving information on genetic associations. These best practice guidelines have been produced to assist clinical laboratories in effectively addressing the complexities of HBOC testing, while taking into account advancements since the last guidelines were published in 2007. These guidelines summarise cancer risk data from recent studies for the most commonly tested high and moderate risk HBOC genes for laboratories to refer to as a guide. Furthermore, recommendations are provided for somatic and germline testing services with regards to clinical referral, laboratory analyses, variant interpretation, and reporting. The guidelines present recommendations where 'must' is assigned to advocate that the recommendation is essential; and 'should' is assigned to advocate that the recommendation is highly advised but may not be universally applicable. Recommendations are presented in the form of shaded italicised statements throughout the document, and in the form of a table in supplementary materials (Table S4). Finally, for the purposes of encouraging standardisation and aiding implementation of recommendations, example report wording covering the essential points to be included is provided for the most common HBOC referral and reporting scenarios. These guidelines are aimed primarily at genomic scientists working in diagnostic testing laboratories.
While tumour mutation burden (TMB) is emerging as a possible biomarker for immune-checkpoint inhibitors (ICI), methods for testing have not been standardised as yet. In April 2019, the International ...Quality Network for Pathology (IQN Path) launched a survey to assess the current practice of TMB testing. Of the 127 laboratories that replied, 69 (54.3%) had already introduced TMB analysis for research purposes and/or clinical applications. Fifty laboratories (72.5%) used targeted sequencing, although a number of different panels were employed. Most laboratories tested formalin-fixed paraffin-embedded material (94.2%), while 18/69 (26%) tested also cell-free DNA. Fifty-five laboratories used both single nucleotide variants and indels for TMB calculation; 20 centers included only non-synonymous variants. In conclusion, the data from this survey indicate that multiple global laboratories were capable of rapidly introducing routine clinical TMB testing. However, the variability of testing methods raises concerns about the reproducibility of results among centers.
Aims
The aim of this proof-of-concept study was to understand the effect of daily intake of a 14-strain probiotic on mood, reward learning and emotional and cognitive processing in adults with low ...mood in the absence of prescribed medication. Salivary cortisol was measured as a marker for physiological stress.
Methods
In this parallel-group double-blind, placebo-controlled trial, 80 healthy adults with self-identified low mood were randomised to receive either the 14-strain probiotic or placebo for a duration of 4 weeks. Data were collected from participants at baseline (week 0) and post-intervention (week 4).
Results
Probiotic intake significantly reduced depression scores (by 50%) compared to baseline, as measured by the Patient Health Questionnaire-9 (PHQ-9) scale (p < 0.05). Analysis of individual items in the PHQ-9 revealed that participants taking probiotics reported improved concentration relative to baseline (+ 51%, p < 0.05) and felt less tired compared to placebo (−21%, p < 0.01).
Regarding emotional processing, the probiotic group was more accurate at recognising facial expressions compared to those receiving placebo (facial emotion recognition test, +12%, p < 0.05). Furthermore, the probiotic group performed less well at the reward learning task relative to the placebo group (probabilistic instrumental learning task, p < 0.05) and was less vigilant to emotional cues compared neutral cues (dot-probe unmasked test, −8%, P < 0.05). The probiotic group also showed increased susceptibility to emotional interference during a cognitive learning task, relative to placebo (auditory visual learning task, −18% p < 0.05).
The study also revealed a downward trend in salivary cortisol in the probiotic group over 4 weeks.
Together, these results suggest that probiotics may work via a different psychological mechanism to that of conventional antidepressants. In other words, probiotics may work by reducing emotional salience across all emotions whereas conventional antidepressants are thought to work by increasing bias to positive emotional cues and decreasing bias to negative ones.
Conclusion
These data suggest that intake of Bio-Kult® Advanced has an effect on mood and that this is achieved in ways distinct from the effects of pharmacological antidepressants. While more research is needed, these results suggest that certain probiotics could form part of an ‘early intervention’ strategy for people experiencing low mood. A second randomised controlled trial (currently recruiting) will provide data on this intervention in patients with a formal diagnosis of depression undergoing concurrent pharmacological treatment.
ClinicalTrials.gov Identifier: NCT03801655
The heartworm Dirofilaria immitis is an important parasite of dogs. Transmitted by mosquitoes in warmer climatic zones, it is spreading across southern Europe and the Americas at an alarming pace. ...There is no vaccine, and chemotherapy is prone to complications. To learn more about this parasite, we have sequenced the genomes of D. immitis and its endosymbiont Wolbachia. We predict 10,179 protein coding genes in the 84.2 Mb of the nuclear genome, and 823 genes in the 0.9‐Mb Wolbachia genome. The D. immitis genome harbors neither DNA transposons nor active retrotransposons, and there is very little genetic variation between two sequenced isolates from Europe and the United States. The differential presence of anabolic pathways such as heme and nucleotide biosynthesis hints at the intricate metabolic interrelationship between the heartworm and Wolbachia. Comparing the proteome of D. immitis with other nematodes and with mammalian hosts, we identify families of potential drug targets, immune modulators, and vaccine candidates. This genome sequence will support the development of new tools against dirofilariasis and aid efforts to combat related human pathogens, the causative agents of lymphatic filariasis and river blindness.—Godel, C., Kumar, S., Koutsovoulos, G., Ludin, P., Nilsson, D., Comandatore, F., Wrobel, N., Thompson, M., Schmid, C. D., Goto, S., Bringaud, F., Wolstenholme, A., Bandi, C., Epe, C., Kaminsky, R., Blaxter, M., Mäser, P. The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets. FASEB J. 26, 4650–4661 (2012). www.fasebj.org
PDF
