The Advantage of Targeted Next-Generation Sequencing over qPCR in Testing for Druggable EGFR Variants in Non-Small-Cell Lung Cancer.

The emergence of targeted therapies in non-small-cell lung cancer (NSCLC), including inhibitors of epidermal growth factor receptor (EGFR) tyrosine kinase, has increased the need for robust companion diagnostic tests. Nowadays, detection of actionable variants in exons 18-21 of the EGFR gene by qPCR and direct DNA sequencing is often replaced by next-generation sequencing (NGS). In this study, we evaluated the diagnostic usefulness of targeted NGS for druggable EGFR variants testing in clinical NSCLC material previously analyzed by the IVD-certified qPCR test with respect to DNA reference material. We tested 59 NSCLC tissue and cytology specimens for EGFR variants using the NGS 'TruSight Tumor 15' assay (Illumina) and the qPCR 'cobas EGFR mutation test v2' (Roche Diagnostics). The sensitivity and specificity of targeted NGS assay were evaluated using the biosynthetic and biological DNA reference material with known allelic frequencies (VAF) of EGFR variants. NGS demonstrated a sufficient lower detection limit for diagnostic applications (VAF < 5%) in DNA reference material; all EGFR variants were correctly identified. NGS showed high repeatability of VAF assessment between runs (CV% from 0.02 to 3.98). In clinical material, the overall concordance between NGS and qPCR was 76.14% (Cohen's Kappa = 0.5933). The majority of discordant results concerned false-positive detection of EGFR exon 20 insertions by qPCR. A total of 9 out of 59 (15%) clinical samples showed discordant results for one or more EGFR variants in both assays. Additionally, we observed TP53 to be a frequently co-mutated gene in EGFR-positive NSCLC patients. In conclusion, targeted NGS showed a number of superior features over qPCR in EGFR variant detection (exact identification of variants, calculation of allelic frequency, high analytical sensitivity), which might enhance the basic diagnostic report.

Computational Tools to Assist in Analyzing Effects of the SERPINA1 Gene Variation on Alpha-1 Antitrypsin (AAT).

In the rapidly advancing field of bioinformatics, the development and application of computational tools to predict the effects of single nucleotide variants (SNVs) are shedding light on the molecular mechanisms underlying disorders. Also, they hold promise for guiding therapeutic interventions and personalized medicine strategies in the future. A comprehensive understanding of the impact of SNVs in the SERPINA1 gene on alpha-1 antitrypsin (AAT) protein structure and function requires integrating bioinformatic approaches. Here, we provide a guide for clinicians to navigate through the field of computational analyses which can be applied to describe a novel genetic variant. Predicting the clinical significance of SERPINA1 variation allows clinicians to tailor treatment options for individuals with alpha-1 antitrypsin deficiency (AATD) and related conditions, ultimately improving the patient's outcome and quality of life. This paper explores the various bioinformatic methodologies and cutting-edge approaches dedicated to the assessment of molecular variants of genes and their product proteins using SERPINA1 and AAT as an example.

Diagnostic and therapeutic value of human serpin family proteins.

SERPIN (serine proteinase inhibitors) is an acronym for the superfamily of structurally similar proteins found in animals, plants, bacteria, viruses, and archaea. Over 1500 SERPINs are known in nature, while only 37 SERPINs are found in humans, which participate in inflammation, coagulation, angiogenesis, cell viability, and other pathophysiological processes. Both qualitative or quantitative deficiencies or overexpression and/or abnormal accumulation of SERPIN can lead to diseases commonly referred to as "serpinopathies". Hence, strategies involving SERPIN supplementation, elimination, or correction are utilized and/or under consideration. In this review, we discuss relationships between certain SERPINs and diseases as well as putative strategies for the clinical explorations of SERPINs.

1.15 Mb microdeletion in chromosome band 20p13 associated with moderate developmental delay-additional case and data's review.

We report on a 9-year-old girl with subtelomeric 20p microdeletion. She was referred for genetic counseling because of learning difficulties/school problems. During the evaluation short stature, hypoplastic fingernails, submucous cleft palate with cleft uvula, flat feet, and frequent upper respiratory infections, as well as the large fontanelle after birth were observed. No facial dysmorphic features specific for chromosomal aberrations were present. The diagnosis of deletion of 20p13 was established by MLPA, and delineated by arrayCGH. Our report describes the third individual with this approximate deletion, and presents detailed molecular and phenotypic characteristics providing new data supporting future genotype-phenotype study.

What are we afraid of when we fear for our health? The symptom context of hypochondriacal complaints. / Czego sie boimy bojac sie o swoje zdrowie? Kontekst objawowy skarg hipochondrycznych.

OBJECTIVES: To identify the set of symptoms most frequently co-occurring with hypochondriacal complaints in patients with neurotic or personality disorders. METHODS: Nonparametric Spearman rank correlations between the variables of symptom checklist "O" describing hypochondriacal symptoms and other symptoms were analyzed. To increase the reliability of the results, the analyses were performed independently in two groups: 3,929 patients before admission to a day hospital in the years 1980-2002 (group A) and 3,190 patients before admission in the years 2004-2015 (group B). RESULTS: For selected groups of patients, lists of correlation coefficients were obtained showing the most important (strongest) and statistically significant associations between five hypochondriacal symptoms and somatization symptoms coming from the muscular system, breathlessness, symptoms coming from the cardiovascular system, anxiety symptoms, and compulsive thoughts without specific content. CONCLUSIONS: The multidimensional nature of hypochondriacal complaints and their association with somatization symptoms similar to infection or inflammation were confirmed. Apart from the fears about patient's own health, fears about close relatives are also an important symptom, to which clinical attention should be paid.

Clinical heterogeneity of polish patients with KAT6B-related disorder.

BACKGROUND: Say-Barber-Biesecker-Young-Simpson (SBBYSS) variant of Ohdo syndrome is a rare, autosomal dominant and clinically heterogenous disorder, caused by pathogenic variants in the KAT6B gene located on chromosome 10q22.2. KAT6B encodes a highly conserved histone acetyltransferase belonging to the MYST family. Currently, diseases caused by pathogenic variants in KAT6B (KAT6B-related disorders) comprise two allelic entities: SBBYSS variant of Ohdo syndrome and genitopatellar syndrome (GPS). Increase in the number of cases with overlapping GPS/SBBYSS phenotype which makes it necessary to redefine this group of phenotypes as KAT6B-related disorders or KAT6B spectrum disorders. Individuals with SBBYSS usually present with facial abnormalities, hypotonia, joint laxity, feeding problems, and long thumbs/great toes. This syndrome also typically involves skeletal problems including patellar hypoplasia/agenesis. METHODS: Here we report six SBBYS syndrome patients with the same dysmorphic features but a different course of the disease. One known and five novel KATB6 pathogenic variants were identified by molecular diagnostics using Next Generation Sequencing (NGS). RESULTS: We present a detailed phenotypic analysis of six individuals with KAT6B-related disorders, in whom a heterozygous pathogenic variant in KAT6B gene was found. In all of our patients facial dysmorphism as well as developmental and speech delay were present. Additionally, all but one patients presented with hypotonia, ocular abnormalities and long thumbs. Most of our probands showed blepharophimosis and skeletal (mainly knee) defects. Contrary to previously reported severe patellar defects (hypoplasia/agenesis) anomalies presented by our patients were less severe (dysplasia, habitual dislocation, subluxation) referring to KAT6B-related disorders. CONCLUSION: While most of the anomalies found in our patients comply with SBBYSS criteria, phenotypic differences in our probands support a broader spectrum of the disease phenotype. To establish the range of this spectrum, a detailed analysis of clinical variability among patients with SBBYSS requires further investigation.

Complaints of dyspnea and their associations with personality traits in patients referred to psychotherapy in a day hospital.

BACKGROUND: Breathing difficulties are present in different medical conditions, yet seem to be underresearched in psychiatric patients. AIM: Assessment of prevalence of dyspnea complaints and their associations with personality traits in patients with neurotic or personality disorders referred to psychotherapy. METHODS: Retrospective chart review of medical records of 2450 patients with diagnoses F4-F6 (ICD-10). Analyses of associations between dyspnea reported in a symptom checklist SCL-O and pathological scores in the Neurotic Personality Questionnaire were carried out using univariate and multivariate regression analyses with ORs and 95%CI estimated with licensed STATISTICA 13 (StatSoftPL) software, and R version 4.1.0, RStudio version 1.4.1717 software. RESULTS: Dyspnea was reported by 46.3% women and 36.6% men (14.5% and 10.1% respectively assessed it as severely burdensome). Univariate regression analysis revealed several significant associations between reporting dyspnea or its extreme intensity and pathological scores in the NPQ. Multivariate regression analyses in women confirmed the importance of impulsiveness and exaltation for dyspnea occurrence, and feeling of being dependent on the environment, demobilization, and narcissistic attitude for its extreme intensity. In men impulsiveness, sense of being in danger, irrationality, and ponderings were associated with the presence of dyspnea, and sense of being in danger and envy with its extreme intensity. CONCLUSIONS: Complaints of dyspnea were pretty frequent. Several personality traits measured by the NPQ questionnaire were predictors of their occurrence and feeling of extreme burden.

Rare clinical findings in three sporadic cases of Beckwith-Wiedemann syndrome due to novel mutations in the CDKN1C gene.

Beckwith-Wiedemann syndrome (BWS) is a rare congenital overgrowth disorder characterised by macroglossia, abdominal wall defects, neonatal hypoglycaemia, lateralised overgrowth and predisposition to embryonal tumours. BWS results mainly from epigenetic changes at chromosome 11p15.5; however, heterozygous pathogenic variants on the maternal CDKN1C allele are observed in 5-8% of sporadic BWS cases. In this study, we report three sporadic BWS patients with novel pathogenic variants in the CDKN1C gene, including one missense (c.181T>C) and two frameshift (c.415_416dup, c.804delC). Detailed clinical evaluation of the patients showed variable manifestation of the disease and underlined the diagnostic challenge for BWS patients at various age of life. The child with the c.415_416dup variant presented with two rare features observed so far in only a few BWS patients with CDKN1C pathogenic variants: supernumerary flexion creases and agenesis of corpus callosum. Confirmation of these findings in another BWS patient adds to the broad clinical spectrum of the disease and suggests that presence of these features may be associated with CDKN1C pathogenic variants.

Novel pathogenic variant in the HRAS gene with lethal outcome and a broad phenotypic spectrum among Polish patients with Costello syndrome.

Costello syndrome (CS) is a rare congenital disorder from the group of RASopathies, characterized by a distinctive facial appearance, failure to thrive, cardiac and skin anomalies, intellectual disability, and a predisposition to neoplasia. CS is associated with germline mutations in the proto-oncogene HRAS, a small GTPase from the Ras family. In this study, a molecular and clinical analysis was carried out in eight Polish patients with the Costello phenotype. A molecular test showed two known heterozygous mutations in the first coding exon of the gene in seven patients: p.G12S (n=4) and p.G12A (n=3), and a novel pathogenic variant p.G60V in one child with an unusually severe, lethal course of the syndrome. In addition, a fatal course of CS was present in one patient with the p.G12A mutation and in another with p.G12S, there was a co-occurrence of Turner syndrome because of the distal Xp deletion. A severe clinical manifestation with a lethal outcome in an individual with p.G60V in HRAS and contrary observations of an attenuated phenotype in CS patients with other mutations at glycine-60 residue may suggest that the nature of the substituted amino acid plays a significant role in the clinical variability observed in some CS cases.

Recombinant growth hormone therapy in a girl with Costello syndrome: a 4-year observation.

BACKGROUND: Costello syndrome is a rare syndrome of multiple congenital anomalies. The typical clinical traits include dysmorphic craniofacial features, skin hyperpigmentation and excess, feeding difficulties leading to severe postnatal growth retardation, short stature, joint hypermobility, and delayed psychomotor development. Additionally, Costello syndrome may present with an increased incidence of congenital heart disease, hypertrophic cardiomyopathy, and increased risk of both benign and malignant tumors. Furthermore, cases of patients with endocrine disorders such as adrenal insufficiency and endogenous growth hormone deficiency have also been documented. CASE PRESENTATION: We present a patient with Costello syndrome who has been successfully treated with recombinant human growth hormone (rhGH) for almost 4 years. CONCLUSIONS: The possibility of growth hormone (GH) treatment can be considered in cases of documented GH deficiency in patients with Costello syndrome, but only under close oncologic and cardiologic supervision.

Oculocutaneous albinism in a patient with 17p13.2-pter duplication - a review on the molecular syndromology of 17p13 duplication.

BACKGROUND: Chromosomal duplications involving 17p13.3 have recently been defined as a new distinctive syndrome with several diagnosed patients. Some variation is known to occur in the breakpoints of the duplicated region and, consequently, in the phenotype as well. AIMS: We report on a patient, the fifth to our knowledge, a 4-year-old girl with a pure de novo subtelomeric 17p13.2-pter duplication. She presents all of the facial features described so far for this duplication and in addition, a unilateral palmar transversal crease and oculocutaneous albinism which has not been reported previously. METHODS: A detailed molecular description of the reported aberration and correlation with the observed phenotypical features based on a literature review. We discuss the possible molecular etiology of albinism in regard to the mode of inheritance. CONCLUSION: The new data provided here may be useful for further genotype correlations in syndromes with oculocutaneous albinism, especially of autosomal dominant inheritance.

Is diagnosing cardio-facio-cutaneous (CFC) syndrome still a challenge? Delineation of the phenotype in 15 Polish patients with proven mutations, including novel mutations in the BRAF1 gene.

Cardio-facio-cutaneous (CFC) syndrome is characterized by a variable degree of developmental delay and congenital anomalies, including characteristic facial, cardiac, and ectodermal abnormalities. It is caused by activating mutations in the Ras/mitogen-activated protein kinase (MAPK) signaling pathway. In, however, approximately 10%-30% of individuals with a clinical diagnosis of CFCS, no mutation of the causative gene is found. Therefore, clinical studies in patients with the CFCS spectrum are valuable. To investigate the phenotypic spectrum and molecular diversity of germline mutations affecting genes encoding serine/threonine kinases, a group of 15 children and young adults with a diagnosis of CFCS was screened. We documented three novel mutations in the BRAF gene and correlated clinical findings with causative mutations in the BRAF or MEK1/MEK2 genes.

Spectrum of JAG1 gene mutations in Polish patients with Alagille syndrome.

Alagille syndrome (ALGS) is an autosomal dominant disorder characterized by developmental abnormalities in several organs including the liver, heart, eyes, vertebrae, kidneys, and face. The majority (90-94%) of ALGS cases are caused by mutations in the JAG1 (JAGGED1) gene, and in a small percent of patients (∼1%) mutations in the NOTCH2 gene have been described. Both genes are involved in the Notch signaling pathway. To date, over 440 different JAG1 gene mutations and ten NOTCH2 mutations have been identified in ALGS patients. The present study was conducted on a group of 35 Polish ALGS patients and revealed JAG1 gene mutations in 26 of them. Twenty-three different mutations were detected including 13 novel point mutations and six large deletions affecting the JAG1 gene. Review of all mutations identified to date in individuals from Poland allowed us to propose an effective diagnostic strategy based on the mutations identified in the reported patients of Polish descent. However, the distribution of mutations seen in this cohort was not substantively different than the mutation distribution in other reported populations.

Cryptic x; autosome translocation in a boy--delineation of the phenotype.

Chromosome X-to-autosome translocations [t(X;A)] are rare rearrangements with an estimated occurrence of 1 to 3 per 10,000 live births. Occurrences of Xq duplications have been observed in male and female subjects in whom the X chromosome segment escapes inactivation and results in functional disomy. We report a case of X;6 translocation in a 7-year-old boy with severe mental retardation, hypotonia, and recurrent respiratory tract infections. High-resolution chromosome analyses (fluorescence in situ hybridization, multiplex ligation probe-dependent amplification, and whole-genome array) revealed a terminal duplication of chromosome X at q28-qter (approximately 3.246 Mb in size) involving gene MECP2 and a terminal deletion (approximately 1.89 Mb) with the breakpoint at 6q27. This is the second report of a boy with a cryptic unbalanced Xq-autosome translocation. This case increases our understanding of mental disability caused by terminal Xq duplication.