Cytoplasmic P53 Immunostaining With N-Terminus P53 Antibody And Absence Of Staining With C-Terminus P53 Antibody: A Report Of Two Pediatric Sarcomas With Distal Truncating Mutations Affecting Nuclear Localization Domain.

P53 immunohistochemical staining with antibodies targeted to epitopes at or near the N-terminus are commonly used in diagnostic pathology practice as a surrogate for mutations. The abnormal staining patterns indicating mutations include nuclear overexpression, null, and the recently described cytoplasmic staining. The latter staining pattern occurs with the less common mutations affecting its nuclear localization and/or tetramerization domains that are located toward the C-terminus.

Germline and sporadic mTOR pathway mutations in low-grade oncocytic tumor of the kidney.

Low-grade oncocytic tumor (LOT) of the kidney is a recently described entity with poorly understood pathogenesis. Using next-generation sequencing (NGS) and complementary approaches, we provide insight into its biology. We describe 22 LOT corresponding to 7 patients presenting with a median age of 75 years (range 63-86 years) and male to female ratio 2:5.

Control Charting Genomic Data.

Background: Control charting is routine in the quality assurance of traditional clinical laboratory testing. Genomic tests are not typically managed by control charting. We examined control charting to monitor the performance of a clinical next-generation sequencing (NGS) assay.

Clinical Validation of a SARS-CoV-2 Real-Time Reverse Transcription PCR Assay Targeting the Nucleocapsid Gene.

Background: Detection of SARS-CoV-2 viral RNA is important for the diagnosis and management of COVID-19.

Methods: We present a clinical validation of a reverse transcription PCR (RT-PCR) assay for the SARS-CoV-2 nucleocapsid (N1) gene. Off-board lysis on an automated nucleic acid extraction system was optimized with endemic coronaviruses (OC43 and NL63).

Hb Alcorn County: A β-Globin Variant [β40(C6)Arg→Thr; : c.122G>C (p.Arg41Thr)] with Increased Oxygen Affinity.

We describe Hb Alcorn County, a heterozygous hemoglobin (Hb) variant, in a 6-month-old Hispanic male and his mother. DNA sequencing demonstrated a mutation on the gene [β40(C6)Arg→Thr; : c.122G>C (p.

Correction to: Molecular characterization of a human group C rotavirus detected first in Turkey.

This article was unintentionally published twice in this journal, by the same authors. Following should be considered the version of record and used for citation purposes: "Mitui, M.T.

Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next-Generation Sequencing Bioinformatics and Variant Interpretation.

Next-generation sequencing is becoming increasingly common in clinical laboratories worldwide and is revolutionizing clinical molecular testing. However, the large amounts of raw data produced by next-generation sequencing assays and the need for complex bioinformatics analyses present unique challenges. Proficiency testing in clinical laboratories has traditionally been designed to evaluate assays in their entirety; however, it can be alternatively applied to separate assay components.

Helicobacter pylori Clarithromycin Resistance and Treatment Failure Are Common in the USA.

Background: Helicobacter pylori antibiotic resistance leads to frequent treatment failure. However, the current US prevalence of H. pylori clarithromycin resistance and treatment failure is unknown.

Characterization of the HBB: c.*233G > C Variant: No Evidence of a β-Thalassemic Phenotype.

β-Thalassemia (β-thal) results from homozygous or compound heterozygous inheritance of β-globin alleles that yield decreased or absent synthesis of the β chain. Disease is frequently severe, requiring lifelong transfusion therapy. Heterozygosity for a β-thal allele results in an asymptomatic carrier state with mild but characteristic hematological findings.

Dominance of emerging G9 and G12 genotypes and polymorphism of VP7 and VP4 of rotaviruses from Bhutanese children with severe diarrhea prior to the introduction of vaccine.

A prospective study was performed to determine the molecular characteristics of rotaviruses circulating among children aged <5 years in Bhutan. Stool samples were collected from February 2010 through January 2011 from children who attended two tertiary care hospitals in the capital Thimphu and the eastern regional headquarters, Mongar. The samples positive for rotavirus was mainly comprised genotype G1, followed by G12 and G9.

Novel Helicobacter pylori sequencing test identifies high rate of clarithromycin resistance.

Objectives: Eradication therapy selection for Helicobacter pylori gastritis requires knowledge of the local resistance rate to clarithromycin. There is minimal population-based or regional data in the United States on pediatric clarithromycin resistance. Although commercial methods such as fluorescence in situ hybridization and DNA probe assays are available in Europe for the evaluation of H pylori 23S rRNA mutations associated with resistance, clinical testing for 23S rRNA in the United States is not widely available.

β-Globin gene sequencing of hemoglobin Austin revises the historically reported electrophoretic migration pattern.

Context: Hemoglobin (Hb) Austin was defined in 1977, using amino acid sequencing of samples from 3 unrelated Mexican-Americans, as a substitution of serine for arginine at position 40 of the β-globin chain (Arg40Ser). Its electrophoretic migration on both cellulose acetate (pH 8.4) and citrate agar (pH 6.

Human bocavirus in patients with encephalitis, Sri Lanka, 2009-2010.

We identified human bocavirus (HBoV) DNA by PCR in cerebrospinal fluid from adults and children with encephalitis in Sri Lanka. HBoV types 1, 2, and 3 were identified among these cases. Phylogenetic analysis of HBoV1 strain sequences found no subclustering with strains previously identified among encephalitis cases in Bangladesh.

Detection and molecular characterization of diarrhea causing viruses in single and mixed infections in children: a comparative study between Bangladesh and Turkey.

The incidence and mortality caused by diarrhea differ among countries. The prevalence of different enteric viruses, their molecular characteristics, and infections with multiple viruses might affect the disease incidence and mortality caused by diarrhea. The objective of this study was to determine the distribution and molecular characteristics of enteric viruses in children with diarrhea in Turkey and Bangladesh.

Development and validation of a quantitative real time PCR assay for BK virus.

Several studies have shown that BK viral load in plasma and urine are reliable markers for the detection of BK virus associated nephropathy (BKVAN) in renal transplant patients. We developed a quantitative real time PCR assay based on TaqMan technology for the measurement of BK viral load in plasma and urine. Considering the high similarity of the nucleotide sequence of the BK virus (BKV) with the JC virus (JCV), we designed this assay to specifically amplify BKV.

Complete Genome Sequence of an MLB2 Astrovirus from a Turkish Child with Diarrhea.

Only two complete genome sequences of MLB2 astroviruses are available, one from an Indian child with diarrhea and another from plasma of an American child. Here we report the complete MLB2 genome sequence from a Turkish child with diarrhea. This MLB2 astrovirus genome sequence shows high nucleotide identity with the American MLB2.

Complete Genome Sequences of Two Astrovirus MLB1 Strains from Bhutanese Children with Diarrhea.

In addition to the eight genotypes of classic human astroviruses, seven new genotypes have been reported from two novel clades, MLB and VA. However, the epidemiology of these highly diverse astroviruses remains largely unknown. We report here the complete genome sequences of two MLB1 strains from Bhutanese children with diarrhea.

Circulating rotaviral RNA in children with rotavirus antigenemia.

Background: Rotavirus antigenemia is a common phenomenon in children with rotavirus diarrhea, but information is scarce on aspects of this phenomenon, such as genotype specificity, presence of intact viruses and correlation between genomic RNA and antigen concentration. Such information may help in understanding rotavirus pathogenesis and eventually be useful for diagnosis, treatment and prevention.

Methods And Findings: Serum samples were collected from children who presented at hospitals with diarrhea.

Long-range PCR based sequencing of the highly homologous genes, SFTPA1 and SFTPA2.

In humans, Surfactant Protein A exists as two highly homologous genetic isoforms, SFTPA1 and SFTPA2. Mutations in these two genes are associated with idiopathic pulmonary fibrosis (IPF) and lung cancer. We have developed a Sanger DNA sequencing assay which utilizes long-range PCR to detect mutations in these two genes.

Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch.

Reverse transcription (RT)-PCR is now the standard method for typing group A rotaviruses (RVA) to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch.

Determination of exposure of dispensary drug preparers to cyclophosphamide by passive sampling and liquid chromatography with tandem mass spectrometry.

Objectives: To determine cyclophosphamide exposure to preparers during tablet crushing and subsequent handling by analyzing indoor air collected using a high-performance volatile organic compounds-solvent desorption (VOC-SD) passive air sampler.

Methods: The passive sampler was taped to the mask over the mouth of the preparer and indoor air was collected during crushing and preparation of cyclophosphamide tablets (Endoxan®). After collection, the carbon molecular sieve adsorbent of the passive sampler was placed in a centrifuge tube, and 1 mL of carbon disulfide was used to elute cyclophosphamide from the adsorbent.

Evaluation of an improved rapid neutralizing antibody detection test (RAPINA) for qualitative and semiquantitative detection of rabies neutralizing antibody in humans and dogs.

Using the principle of immunochromatography, we previously developed a method called RAPINA (Rapid Neutralizing Antibody detection test) that can measure the level of rabies virus -neutralizing antibody (VNA) in serum samples [Shiota S, Mannen K, Matsumoto T, Yamada K, Yasui T, Takayama K, et al. Development and evaluation of a rapid neutralizing antibody test for rabies. J Virol Methods 2009;161:58-62].

Immunohistochemical expression of GLUT1 and its correlation with unfavorable histology and TP53 codon 72 polymorphism in Wilms tumors.

Reprogramming of energy metabolism, such as increased glycolysis, is a hallmark of cancer cells. One mechanism by which cancer cells fuel glycolysis is through increased uptake of glucose across cell membranes via the glucose transporter GLUT1. One of the transcriptional repressors of GLUT1 is wild-type TP53, and cancer-associated loss of function mutations within the DNA-binding domain of TP53 impairs the repressive effect of TP53 on transcriptional activity of the GLUT1 gene promoter.