Uticaj supstituenata na IR, 1H- i 13C-NMR spektralne podatke N-(supstituisanih fenil)-2-cijanoacetamida - korelaciona analiza

Linear free energy relationships (LFER) were applied to the IR, H-1- and C-13-NMR spectral data of N-(substituted phenyl)-2-cyanoacetamides. A variety of substituents were employed for phenyl substitution and fairly good correlations were obtained using the simple Hammett and the Hammett-Taft dual substituent parameter equations. The correlation results of the substituent induced C-13-NMR chemical shifts (SCS) of the Cl, C=O and N-H atom indicated different sensitivity with respect to electronic substituent effects. A better correlation of the SCSc=O with a combination of electrophllic and nucleophilic substituent constants indicated a significant contribution of extended resonance interaction (pi-delocalization) within the pi(1)-unit. The conformations of the investigated compounds were studied using the OFT B3LYP/6-311G** method and, together with the results of C-13-NMR and IR spectroscopic studies, a better insight into the influence of such a structure on the transmission of electronic substituent effects was obtained.Principi linearnih korelacija slobodnih energija (LFER) su primenjeni na IR, 1H- i 13C-NMR spektralne podatke N-(supstituisanih fenil)-2-cijanoacetamida. Pri sintezi N-(supstituisanih fenil)-2-cijanoacetamida izvršen je zadovoljavajući izbor supstituenata u pogledu elektronskih svojstava kako bi se adekvatno sagledao uticaj elektronskih efekata supstituenata na pomeranja u IR, 1H- i 13C-NMR spektralnim podacima. Primenom proste Hametove jednačine dobijene su zadovoljavajuće korelacije. Na osnovu korelacionih rezultata uočen je primaran uticaj elektronskih efekata na SCS (supstituentom indukovana hemijska pomeranja) vrednosti N-H vodonika, C1 i C=O ugljenika ispitivanih jedinjenja. Korelacioni rezultati za C=O ugljenik se značajno popravljaju ako se koristi kombinacija Ϭ+ i Ϭ- konstanti supstituenata, takozvane elektrofilne i nukleofilne konstante supstituenata, što ukazuje na postojanje značajne proširene rezonancione interakcije supstituenata i elektronske gustine karbonilne grupe. Vrednosti konstanti proporcionalnosti pF i pR za sve atome, ukazuju na približno isti doprinos efekta polja i rezonancionog efekta supstituenata. Efekat polja je nešto izraženji na N-H vodoniku, i za sve atome pokazuje značajne razlike u odnosu na njihov položaj u molekulskoj strukturi ispitivanih jedinjenja. Uticaj efekata supstituenata na IR vibracije istezanja N-H (simetrične i antisimetrične), C=O i CN veze je prevashodno elektronske prirode što se može zaključiti na osnovu dobrih korelacija dobijenih primenom Hametove jednačine i Ϭ parametara supstituenata. Osim toga izvršena je optimizacija geometrije ispitivanih jedinjenja primenom DFT B3LYP/ 6-311G**metode, pri čemu je nađeno da je trans-izomer nešto stabilnji, izuzev u slučaju jedinjenja 3. Supstituisana fenil-grupa i amidna grupa, kod trans-izomera, su približno koplanarne, dok se kod cis- izomera uočava značajna devijacija koja je značajno određena elektronskim efektima prisutnog supstituenta. Takođe je ispitivan položaj cis/trans ravnoteže u ugjen-tetrahloridu, i na osnovu rezultata FT/R analize, kada je prisutan H, CH3, OCH3, Br, i COOH supstituent, nađeno je da je cis izomer u velikom višku, a za ostala jedinjenja utvrđeno je postojanje ravnoteže cis- i trans-izomera

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort

PURPOSE: Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes. METHODS: Clinical data was collected through an extensive web-based survey. RESULTS: We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%). CONCLUSION: Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes

Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort

Purpose: Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes.Methods: Clinical data was collected through an extensive web-based survey.Results: We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%).Conclusion: Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes. (C) 2022 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.Genetics of disease, diagnosis and treatmen

Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort

Purpose: Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes. Methods: Clinical data was collected through an extensive web-based survey. Results: We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%). Conclusion: Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes

The expanding spectrum of COL2A1 gene variants IN 136 patients with a skeletal dysplasia phenotype

International audienceHeterozygous COL2A1 variants cause a wide spectrum of skeletal dysplasia termed type II collagenopathies. We assessed the impact of this gene in our French series. A decision tree was applied to select 136 probands (71 Stickler cases, 21 Spondyloepiphyseal dysplasia congenita cases, 11 Kniest dysplasia cases, and 34 other dysplasia cases) before molecular diagnosis by Sanger sequencing. We identified 66 different variants among the 71 positive patients. Among those patients, 18 belonged to multiplex families and 53 were sporadic. Most variants (38/44, 86%) were located in the triple helical domain of the collagen chain and glycine substitutions were mainly observed in severe phenotypes, whereas arginine to cysteine changes were more often encountered in moderate phenotypes. This series of skeletal dysplasia is one of the largest reported so far, adding 44 novel variants (15%) to published data. We have confirmed that about half of our Stickler patients (46%) carried a COL2A1 variant, and that the molecular spectrum was different across the phenotypes. To further address the question of genotype-phenotype correlation, we plan to screen our patients for other candidate genes using a targeted next-generation sequencing approach.European Journal of Human Genetics advance online publication, 2 December 2015; doi:10.1038/ejhg.2015.25