Noninvasive prenatal diagnosis of genetic diseases induced by triplet repeat expansion by linked read haplotyping and Bayesian approach

The field of noninvasive prenatal diagnosis (NIPD) has undergone significant progress over the last decade. Direct haplotyping has been successfully applied for NIPD of few single-gene disorders. However, technical issues remain for triplet-repeat expansions. The objective of this study was to develop an NIPD approach for couples at risk of transmitting dynamic mutations. This method includes targeted enrichment for linked-read libraries and targeted maternal plasma DNA sequencing. We also developed an innovative Bayesian procedure to integrate the Hoobari fetal genotyping model for inferring the fetal haplotype and the targeted gene variant status. Our method of directly resolving parental haplotypes through targeted linked-read sequencing was smoothly performed using blood samples from families with Huntington’s disease or myotonic dystrophy type 1. The Bayesian analysis of transmission of parental haplotypes allowed defining the genotype of five fetuses. The predicted variant status of four of these fetuses was in agreement with the invasive prenatal diagnosis findings. Conversely, no conclusive result was obtained for the NIPD of fragile X syndrome. Although improvements should be made to achieve clinically acceptable accuracy, our study shows that linked-read sequencing and parental haplotype phasing can be successfully used for NIPD of triplet-repeat expansion diseases.

Trial registration: NCT04698551_date of first registration: 07/01/2021.

X-autosome and X-Y Translocations in Female Carriers: X-chromosome Inactivation Easily Detectable by 5-ethynyl-2-deoxyuridine (EdU)

Here we report one new case each of an X-autosome translocation (maternally derived), and an X-Y-chromosome translocation. Besides characterizing the involved breakpoints and/or imbalances in detail by molecular cyto-genetics, also skewed X-chromosome inactivation was determined on single cell level using 5-ethynyl-2-deoxyuridine (EdU). Thus, we confirmed that the recently suggested EdU approach can be simply adapted for routine diagnostic use. The latter is important, as only by knowing the real pattern of the skewed X-chromosome inactivation, correct interpretation of obtained results and subsequent reliable genetic counseling, can be done.

Pepper: cytoscape app for protein complex expansion using protein-protein interaction networks

We introduce Pepper (Protein complex Expansion using Protein–Protein intERactions), a Cytoscape app designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the coverage, a solution must contain as many proteins from the seed as possible, (ii) the density, the proteins of a solution must be as connected as possible, using only interactions from a proteome-wide interaction network. Comparisons based on gold standard yeast and human datasets showed Pepper’s integrative approach as superior to standard protein complex discovery methods. The visualization and interpretation of the results are facilitated by an automated post-processing pipeline based on topological analysis and data integration about the predicted complex proteins. Pepper is a user-friendly tool that can be used to analyse any list of proteins.

Availability: Pepper is available from the Cytoscape plug-in manager or online (http://apps.cytoscape.org/apps/pepper) and released under GNU General Public License version 3.

Contact: mohamed.elati@issb.genopole.fr

Supplementary information:Supplementary data are available at Bioinformatics online.

Measuring inspiratory muscle strength in neuromuscular disease: one test or two?

Inspiratory muscle strength monitoring is crucial in patients with neuromuscular disorders. The sniff nasal inspiratory pressure (SNIP) and maximal inspiratory pressure (P(I,max)) are usually measured. The present study investigated whether the test yielding the best value at baseline continued to yield the best value during follow-up. The present study included 25 patients with Duchenne muscular dystrophy (DMD) and 61 with myotonic muscular dystrophy (MMD). SNIP and P(I,max) were measured at baseline and then annually. At baseline, SNIP was lower than P(I,max) in 20 (80%) DMD patients and 32 (52%) MMD patients. During follow-up in DMD patients, changes in the best method always occurred from SNIP to P(I,max). In MMD patients, when SNIP was better than P(I,max) at baseline, SNIP was usually (88%) better during follow-up, whereas a better P(I,max) than SNIP at baseline was frequently (50%) followed by a shift to SNIP. Maximal inspiratory pressure may be sufficient for monitoring inspiratory muscle function in Duchenne muscular dystrophy adults. In myotonic muscular dystrophy, the marked variability in the test yielding the best value at baseline indicates a need for performance of both tests at baseline. However, when sniff nasal inspiratory pressure measurement yields the best value at baseline, using sniff nasal inspiratory pressure alone during follow-up may be appropriate.

Sniff nasal inspiratory pressure: what is the optimal number of sniffs?

Sniff nasal inspiratory pressure (SNIP) measurement is a volitional noninvasive assessment of inspiratory muscle strength. A maximum of 10 sniffs is generally used. The purpose of the present study was to investigate whether the maximum SNIP improved after the tenth sniff. In total, 20 healthy volunteers and 305 patients with various neuromuscular and lung diseases were encouraged to perform 40 and 20 sniffs, respectively. The best SNIP among the first 10 sniffs was lower than the best SNIP among the next 10 sniffs in the healthy volunteers and patients. The SNIP improvement after the twentieth sniff was marginal. In conclusion, a learning effect persists after the tenth sniff. The current authors suggest using 10 additional sniffs when the best result of the first 10 sniffs is slightly below normal, or when sniff nasal inspiratory pressure is used to monitor a progressive decline in inspiratory muscle strength.

PHYTOPROT: a database of clusters of plant proteins

All the protein sequences from plants (including Arabidopsis thaliana) available from SwissProt/TrEMBL have been the subject of an all-by-all systematic comparison and grouped into clusters of related proteins. Within each cluster, the sequences have been submitted to pyramidal classification; in the case where two or several subfamilies have been grouped together, the pyramidal tree helps in finding which sequences make the links between subfamilies. In addition, the 'domains' that are common to two or more sequences within a cluster were determined and displayed à la ProDom. The resulting graphical representations proved to be quite efficient in pinpointing those protein sequences suffering from a probable error in the annotation of their genes. The clusters can be searched through various criteria and their pyramidal classifications and their domain representations can be displayed by querying http://genoplante-info. infobiogen.fr/phytoprot. The user can also launch a BLAST search of a query sequence against all the clusters.

Polypharmacy (or polytherapy) in the treatment of heart failure

There is now conclusive evidence that most patients with heart failure due to left ventricular systolic dysfunction should be treated with angiotensin converting enzyme (ACE) inhibitors and beta-blockers. They will also need diuretics for the control of fluid retention. There is also a powerful case for adding spironolactone to the treatment of patients with more severe symptoms. Many doctors would also use digoxin and, especially if coronary disease is present, aspirin or warfarin. Most patients also have other chronic diseases, such as diabetes, arthritis, depression and dyspepsia, and each of these may provoke the prescription of yet another agent. Many patients will receive prescriptions to treat the side-effects of their therapy. Finding a sure path through the morass of pharmacotherapy is a daunting task. Polypharmacy is having a negative impact on new drug research in an area where there are in fact remarkably few really effective treatments and the therapeutic problem is only partially solved. This paper discusses some of the issues surrounding polypharmacy in heart failure and how to resolve them, using an illustrative case history. It highlights the potential benefits of polypharmacy with effective drugs and the gross over-use of ineffective treatments in heart failure. The major problem with polypharmacy in heart failure is not the heart failure treatment itself, but the drugs for other concomitant conditions, the effectiveness of which is often not supported by an appropriate evidence base and for which alternative, less noxious management strategies often exist. Polypharmacy may be deleterious not only because of the increased potential for side-effects and drug interactions but also because taking unnecessary therapy reduces compliance with effective drugs.

Deciphering Arabidopsis thaliana gene neighborhoods through bibliographic co-citations

In the framework of genome annotation, scientific literature is obviously the major source of biological knowledge. The aim of the work described in this paper is to exploit this source of data for the model plant Arabidopsis thaliana. The first step has consisted in constituting a relevant bibliographic references dataset for plant genomic research. Genes co-citations have then been systematically annotated in this reference dataset, starting from the simple idea that if genes are cited in the same publication, they must probably share some related functional properties. In order to deal with the synonymous gene name problem, a gene name reference list has been constituted starting from A. thaliana SwissProt entries. This list was used to build clusters of co-cited genes by a single linkage procedure such that any gene in a given cluster possesses at least one co-cited partner in the same cluster. Analysis of the clusters demonstrate the biological consistency of this approach, with only very few fortuitous links. As an example, a cluster including genes related to flowering time is more deeply described in the paper. Finally, a graphical representation of each cluster was performed, which provides a convenient way to retrieve the genes (the nodes of the graphs) and the references in which they were co-cited (the edges of the graphs). All the results can be accessed at the URL http://chlora.Igi.infobiogen.fr:1234/bib_arath/.

An incremental algorithm for Z-value computations

The Z-value (Comput. Chem. 23 (1999) 333) is an extension of the Z-score that is classically used to compare sets of biological sequences. The Z-value has been successfully used to handle complete genome studies as well as analyze large sets of proteins. The Z-value computation is based on a Monte Carlo approach to estimate the statistical significance of a Smith & Waterman alignment score. Comet et al. (Comput. Chem. 23 (1999) 333) have shown that, in contrast to the alignment score, the Z-value largely reduces the bias due to the lengths and compositions of the sequences. They also described an estimator of the deviation of Z-values, that we extend in this paper in order to optimize Z-values computation. The incremental algorithm described here provides two characteristics which are usually incompatible: (i) it improves the accuracy of Z-values calculation; (ii) it reduces the time complexity (this algorithm has been named incremental because it iteratively adds random sequences to the Monte-Carlo process when needed). Results are presented, originating from the all-by-all comparison of the proteins from Saccharomyces cerevisiae and Escherichia coli.

Clinical Trials Update: CAPRICORN, COPERNICUS, MIRACLE, STAF, RITZ-2, RECOVER and RENAISSANCE and cachexia and cholesterol in heart failure. Highlights of the Scientific Sessions of the American College of Cardiology, 2001

This is a synopsis of presentations made at the American College of Cardiology (ACC) in 2001 summarising recent research developments relating to heart failure. Clinical studies of particular interest to physicians with an interest in heart failure and its prevention are reviewed. The COPERNICUS trial lends further support to the use of the beta-blocker, carvedilol, in severe heart failure and the CAPRICORN trial to its use in patients with post-infarction left ventricular systolic dysfunction. The MIRACLE study reinforces the evidence from three smaller trials that cardiac resynchronisation therapy is an effective treatment for the relief of symptoms in patients with severe heart failure and cardiac dyssynchrony. The STAF trial casts further doubt on the wisdom of cardioversion as a routine strategy for the management of chronic atrial fibrillation. The RITZ-2 trial suggests that an intravenous, non-selective endothelin antagonist is effective in improving haemodynamics and symptoms and possibly in reducing morbidity in severe heart failure. Observational studies in heart failure suggest that a moderate excess of body fat and elevated blood cholesterol may be desirable in patients with heart failure, challenging the current non-evidenced-based vogue for cholesterol lowering therapy in heart failure. The RENAISSANCE and RECOVER outcome studies of etanercept, a tumour necrosis factor (TNF) receptor analogue that blocks the effect of TNF, were stopped because of lack of evidence of benefit shortly after the ACC.

Massive sequence comparisons as a help in annotating genomic sequences

An all-by-all comparison of all the publicly available protein sequences from plants has been performed, followed by a clusterization process. Within each of the 1064 resulting clusters-containing sequences that are orthologous as well as paralogous-the sequences have been submitted to a pyramidal classification and their domains delineated by an automated procedure à la. This process provides a means for easily checking for any apparent inconsistency in a cluster, for example, whether one sequence is shorter or longer than the others, one domain is missing, etc. In such cases, the alignment of the DNA sequence of the gene with that of a close homologous protein often reveals (in 10% of the clusters) probable sequencing errors (leading to frameshifts) or probable wrong intron/exon predictions. The composition of the clusters, their pyramidal classifications, and domain decomposition, as well as our comments when appropriate, are available from http://chlora.infobiogen.fr:1234/PHYTOPROT.

[Excerpts from the eulogy of Jean-Louis Petit presented during the public session of the Royal Academy of Surgery on May 26 1750 by A. Louis]

Jean-Louis Petit (1674-1750) was first enthusiastic about anatomy, received a master's certificate in surgery in Paris in 1700, became a member of the Royal Academy of Sciences in 1715, and was named director of the Royal Academy of Surgery by the king when it was created in 1731. He acquired great notoriety because of his skill and experience, thanks to his case reports of hemorrhage, lacrimal fistula, operation on the frenum, for his treatise on bone diseases and especially for his general treatise on surgical operations on which he worked 12 years and which was finished after his death by F.D. Lesne.

[Germain Pichaut de Lamartinière. Eulogy presented to the Royal Academy of Surgery during the public session on April 22, 1784]

G. Pichaut de Lamartinière (1696-1783) accompanied the king during his campaigns and, in 1747, then succeeded La Peyronie as first surgeon to the king and President of the Royal Academy of Surgery. "He devoted his talent as an organizer in favour of surgeons. He did everything to proclaim the independence of surgery and to protect it from the tyranny of the Faculty of Medicine of Paris". He did not leave behind any scientific or academic works.

Preparation of the cerebroside sulfate activator (CSAct or saposin B) from human urine

The purification of cerebroside sulfate activator (CSAct) or saposin B from pooled human urine is described. Urinary proteins are concentrated by ammonium sulfate precipitation. A suspension of the precipitate is heat-treated and the heat-stable proteins are fractionated through a series of chromatographic steps. An initial concanavalin A column retains little of the CSAct activity, but is important for subsequent purification. Passing the Con A effluent directly onto an octyl Sepharose column removes the protein of interest which is recovered by affinity elution with octyl glucoside. Subsequent ion-exchange and gel filtration chromatographies yield a protein of 80-90% purity, although it is sometimes necessary to repeat one or more steps. A small amount of CSAct can sometimes be recovered from the initial Con A Sepharose column by methyl mannoside elution and purified by a parallel chromatographic protocol. Mass spectral analysis suggests that the final material is a mixture of two major and several minor glycoforms of a 79 amino acid protein with the structure predicted from the human prosaposin cDNA by truncation of both N- and C-terminal regions. Sugar analysis revealed the presence of glucosamine, mannose, and fucose, consistent with the major isoforms bearing a five-sugar Man(2)GluNac(2)Fuc or a single GluNac substituent. The human urinary material is similar to the previously characterized pig kidney protein in most respects, but varies in some details.

Drug consumption in workers in France: a comparative study at a 10-year interval (1996 versus 1986)

This study compared drug consumption and associated social factors in workers in France between 1986 and 1996. The same transversal survey was performed in 1986 and 1996 using the same methodology by means of an anonymous questionnaire given to the subject and answered in the presence of an occupational physician. The 1996 population (2674 subjects) was found to be older (37.0 +/- 9.8 versus 35.7 +/-10.2 years) and to take more drugs (+5.1%) than the population of 1986 (2221 subjects). There were fewer manual workers in the 1996 population. In both periods, women used significantly more drugs in general and more psychoactive (mainly anxiolytic), cardiovascular, endocrine metabolic, and homeopathic drugs than men. The mean value of estimated difficulty of work was higher in subjects taking drugs in general, and especially those taking hypnotic, anxiolytic, psychoactive, antiinflammatory, and digestive drugs in 1986 as well in 1996. In 1986 as well as in 1996, manual workers took no more drugs than did nonmanual workers in general, except for analgesic and antiinflammatory drugs. Nonmanual workers used homeopathic drugs more than manual workers. The presence of extraprofessional problems was associated with an increase in consumption of drugs in general and psychoactive, hypnotic, anxiolytic, antiinflammatory, cardiovascular, digestive, and endocrine metabolic drugs in particular, in 1986 as well as in 1996. After adjustment for variables linked to drug use, there was no significant change in total drug consumption in general but a significant decrease in psychoactive (-49%) (mainly hypnotic [-71%]), and digestive (-39%) drug consumption in this population between 1986 and 1996. In contrast, analgesic use significantly increased (+36%). This study underscores the high level of drug consumption in workers (more than 40% of the subjects were taking drugs). Although there were no quantitative changes, marked qualitative modifications were found with a decrease in consumption of psychoactive (and mainly hypnotic) and digestive drugs and an increase in analgesic drug use between 1986 and 1996. Thus, specific drug information programs designed to reduce psychoactive drug consumption and to favor analgesic drugs for better pain management seem to have been (at least partly) followed. The study also underscores the importance of some social factors associated to general and specific drug use (mainly difficulty of work and presence of extraprofessional problems, and to a lesser extent, kind of work). Their weight remained similar in 1986 and 1996.

The development of the Louis MACRO (Mother and Child Risk Observation) forms: assessing parent-infant-child risk in the presence of maternal mental illness

OBJECTIVE

The theoretical framework and psychometric properties of the MACRO (Mother and Child Risk Observation) 1 and 2 forms (age 0 to 4 year) are presented. The MACRO forms provide ratings on five domains--three related to parenting, two on infant (or child) characteristics and maternal mental state. Case vignettes illustrate their clinical utility.

METHOD

Ratings on the MACRO of 110 mother-infant and 85 mother-toddler consecutive admissions to a South Australian psychiatric in-patient mother-infant unit provided data on internal consistency, interrater, and test-retest reliability.

RESULTS

Internal consistency was between .79 and .95 for all MACRO domains. Item-total correlations were between .39 and .90 with the exception of one item. Social Support. Distributions of item scores indicated acceptable discrimination. Interrater reliability was .79 or above for all domains. Test-retest reliability after 7 days was .71 or above.

CONCLUSIONS

Preliminary psychometric investigations of the MACRO was favorable. Should further validity investigations prove satisfactory, the MACRO will provide a valuable clinical and research tool. The MACRO offers a convenient framework for assessing risk and interpreting the impact of maternal mental illness upon children within a context that permits consideration of factors such as illness severity, parenting practices, and child contribution to outcome.

Strategies for optimized application of annular-phased-array systems in clinical hyperthermia

A theoretical framework is presented for optimized heating of deep-seated tumours by phase and amplitude steering. The optimization problem for a specific tumour and perfusion case results in a functional dependency between power-level and maximum obtainable therapeutic efficiency. Different optimization criteria and strategies are outlined, which cause an increase of power or thermal dose in the tumour. Three tumour models (central pelvic tumour, eccentric abdominal tumour with or without necrosis) are analysed in detail. The simulation studies predict that appreciable parts of these tumours (50-100%) can be heated efficiently (42.5-43 degrees C) within the range of available and clinically tolerated power levels (1-5 kW/m), if tumour perfusion is less than 20-25 ml/100 g min. Some improvements are obtained by increasing the number of independent channels (from four to eight) and by the application of time-dependent (complementary) power-deposition patterns.

A longitudinal study of psychotropic prescriptions in a teaching nursing home

This study clarifies the methodological pitfalls of using cross-sectional data to characterize episodic and continuous patterns of prescribing psychotropic medications in nursing homes. Although more than half of the residents in a teaching nursing home received a psychotropic drug during their 5 years of residence, less than one-quarter were continuously medicated. The authors conclude that although the rates of psychotropic prescriptions are an important entry point for concerns about quality and appropriateness of psychotropic administration to older nursing home residents, longitudinal studies including the prescribing pattern, indications, and efficacy are needed to determine more clinically meaningful indicators of quality care.

Leber's disease and dystonia: a mitochondrial disease

We studied a kindred in which 8 members had the neuroretinopathy of Leber's disease; 14 had a progressive, generalized dystonia attributed to striatal degeneration; and 1 had both disorders. The mode of inheritance was compatible with maternal transmission. This neurologic disorder may be a mitochondrial disease.

Penicillinase-producing Neisseria gonorrhoea as a cause of neonatal and adult ophthalmia

A retrospective analysis of 80 cases of gonococcal ophthalmia revealed six (7.5%) to be due to penicillinase-producing Neisseria gonorrhoeae (PPNG), five neonatal cases and one adult. All six cases were finally cured, but best results were obtained with topical chloramphenicol and single-dose spectinomycin (40 mg/kg) given intramuscularly. All gonococcal isolates should be tested promptly for penicillinase production, and if this is present systemic treatment, modified to spectinomycin or penicillinase-stable cephalosporin, should be given as single-dose treatment.

Clinical and prognostic significance of portohepatic gradient in patients with cirrhosis

As the clinical significance of hemodynamic parameters remains controversial, the portohepatic gradient has been measured in 89 patients with cirrhosis by a transjugular approach. Relationships between portohepatic gradient and clinical, roentgenologic and prognostic patterns were studied with a maximum follow-up period of 36 months. Portohepatic gradient was not related to the rate of occurrence or rate of recurrence of digestive tract bleeding. Portohepatic gradient was related to the size of esophageal varices, p less than 0.01. Observation of large varices at endoscopy was associated with a higher risk of digestive tract bleeding. Portohepatic gradient was related to the number of portosystemic shunts opacified at portography, p less than 0.01. Portohepatic gradient was found to be related to these aspects of prognosis: the mean portohepatic gradient was higher in patients who died than it was in survivors, p less than 0.05. When patients were separated into two groups according to portohepatic gradient values--greater than or equal to 20.8, less than 20.8 millimeters of mercury--the actuarial survival rate was inversely related to portohepatic gradient at one, p less than 0.02, and at 12, p less than 0.02, months of follow-up study. This relationship could be demonstrated in the entire group of patients with cirrhosis and in the group of patients with digestive tract bleeding. This pattern seemed to be related to the risk of hemorrhage. In groups of patients and within a 24 month observation period, the survival rate was significantly related to the range of portohepatic gradient in each group.

Haemostasis disorders in open heart surgery with extracorporeal circulation. Importance of the platelet function and the heparin neutralization

The main haemostasis changes observed in a screening study performed in 40 patients who underwent an open heart surgery with extracorporeal circulation (ECC) are: a significant drop in platelet count from the onset of the ECC to the third postoperative day, a decrease of platelet retention and aggregation during ECC with an 8-day persistently increased heparin-neutralizing activity in plasma but not in serum, a moderate decrease of plasma factors I, II, VII-X, X and XIII and a more important drop in factor V which disappears 24 h after ECC, a transitory increase of fibrinolysis during ECC and the lack of FDP elevation in the serum. These disorders require a very good neutralization of the heparin used during ECC. The ratio protamine/heparin can be established by a titration clotting time test. Protamine chloride seems to be more efficacious and to act more quickly than protamine sulfate for the neutralization. An overload in protamine can enhance the hemostatic, biological and clinical disorders. The preventive administration of platelet concentrate immediately after the heparin neutralization contributes to reduce the bleeding disorders related to the quantitative and qualitative platelet defects.