Activating PIK3CA postzygotic mutations in segmental overgrowth of muscles with bone involvement in the body extremities.

Segmental overgrowth of the skeletal muscles with bone involvement in body extremities, predominantly affecting the upper limb, is an extremely rare condition with only 40-50 affected children described clinically. The molecular pathogenesis of this disorder remains largely unclear except for the identification of a somatic PIK3CA mutation in each of the six patients genetically tested, all restricted to upper limbs in the literature. This study aimed to further characterize the molecular defects for patients affected with segmental overgrowth of the skeletal muscles by analyzing a 9-gene panel selected from the PI3K/AKT/mTOR pathway and genes associated with other related conditions. Nineteen unrelated patients were chosen for this study, comprising ten upper limb (nine unilateral and one bilateral) and nine lower limb (eight unilateral and one bilateral) cases with variable bone involvement. In each case, an activating PIK3CA mutation (p.E110del, p.N345K, p.E542K, p.E545K, p.H1047R, or p.H1047L) was identified in the affected muscle tissue with variant allele frequencies ranging from 13.88 to 30.43%, while no mutation was detected in the paired peripheral blood sample, indicating somatic mosaicism. All detected mutations were limited to PIK3CA and were previously reported in other overgrowth syndromes currently categorized under the PIK3CA-Related Overgrowth Spectrum (PROS). Our study provides strong molecular evidence that isolated segmental overgrowth of the skeletal muscle with bone involvement is a subtype of PROS. Our findings expand the PROS clinical presentations with a newly molecularly classified condition and can provide guidance in clinical and molecular diagnosis and treatment for patients with this condition.

Use of medical exome sequencing for identification of underlying genetic defects in NICU: Experience in a cohort of 2303 neonates in China.

Emerging evidence demonstrates the clinical utility of genomic applications in newborn intensive care unit (NICU) patients with strong indications of Mendelian etiology. However, such applications' diagnostic yield and utility remain unclear for NICU cohorts with minimal phenotype selection. In this study, focused medical exome sequencing was used as a first-tier, singleton-focused diagnostic tool for 2303 unrelated sick neonates. Integrated analysis of single nucleotide variants (SNVs), small insertions and deletions (Indels), and large copy number variants (CNVs) was performed. The diagnostic rate in this NICU cohort is 12.3% (284/2303), with 190 probands with molecular diagnoses made from SNV/Indel analyses (66.9%), 93 patients with diagnostic aneuploidy/CNVs findings (32.8%), and 1 patient with both SNV and CNV (0.4%). In addition, 54 (2.3%) of patients had a reportable incidental finding. Multiple organ involvements, craniofacial abnormalities, and dermatologic abnormalities were the strongest positive predictors for a molecular diagnosis. Among the 190 cases with SNV/Indel defects, direct impacts on medical management were observed in 46.8% of patients after the results were reported. In this study, we demonstrate that focused medical exome sequencing is a powerful first-line diagnostic tool for NICU patients. Significant number of diagnosed NICU patients can benefit from more focused medical management and long-term care.

The Genomic Era of Clinical Oncology: Integrated Genomic Analysis for Precision Cancer Care.

Genomic alterations are important biological markers for cancer diagnosis and prognosis, disease classification, risk stratification, and treatment selection. Chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) technologies are superb new tools for evaluating cancer genomes. These state-of-the-art technologies offer high-throughput, highly accurate, targeted and whole-genome evaluation of genomic alterations in tumor tissues. The application of CMA and NGS technologies in cancer research has generated a wealth of useful information about the landscape of genomic alterations in cancer and their implications in cancer care. As the knowledge base in cancer genomics and genome biology grows, the focus of research is now shifting toward the clinical applications of these technologies to improve patient care. Although not yet standard of care in cancer, there is an increasing interest among the cancer genomics communities in applying these new technologies to cancer diagnosis in the Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories. Many clinical laboratories have already started adopting these technologies for cancer genomic analysis. We anticipate that CMA and NGS will soon become the major diagnostic means for cancer genomic analysis to meet the increasing demands of precision cancer care.

Levels and Profiles of Polybrominated Diphenyl Ethers in Breast Milk During Different Nursing Durations.

Eight PBDE congeners, BDE-28, 47, 99, 100, 153, 154, 183 and 209, were measured using gas chromatography coupled to mass spectrometry. The concentrations of Σ8PBDEs ranged from 0.04 to 19.93 ng g(-1) lipid weight (lw), with median and mean value of 1.21 and 2.72 ng g(-1) lw. PBDE congeners were detected in approximately 90 % of samples with BDE-209 as the dominant one. No significant correlations were found between the mothers' age, body mass index and PBDEs concentrations. We estimated the infant's dietary intake of the studied PBDEs via human milk during different nursing durations, and found that babies younger than 1 month might take a relatively higher body burden of PBDEs. The median levels of Σ8PBDEs were 0.74, 2.80, 2.43 and 0.90 ng g(-1) lw in colostrum, milk sampled at 1, 3 and 6 months after birth, respectively. High consumption of animal-origin food after birth may lead to the elevated ΣPBDEs concentrations in breast milk. A rational nutrition deployment is essential for postpartum mother.

Prenatal diagnosis of CLOVES syndrome confirmed by detection of a mosaic PIK3CA mutation in cultured amniocytes.

Congenital lipomatous asymmetric overgrowth of the trunk, lymphatic, capillary, venous, and combined-type vascular malformations, epidermal nevi, skeletal and spinal anomalies (CLOVES) syndrome, a segmental overgrowth syndrome, is caused by post zygotic somatic mutations in PIK3CA, a gene involved in the receptor tyrosine kinase phosphatidylinositol 3-kinase (PI3)-AKT growth-signaling pathway. Prenatal ultrasound findings of lymphovascular malformations, segmental overgrowth and skeletal defects can raise suspicion for CLOVES syndrome, but molecular confirmation of PIK3CA mutations on prenatally obtained samples is challenging because of somatic mosaicism. We detected a mosaic disease-causing mutation in PIK3CA by sequencing of DNA extracted from cultured amniotic cells, but not from DNA directly prepared from an amniotic fluid sample in a fetus with prenatally suspected CLOVES syndrome. The infant was born prematurely and displayed severe lymphovascular malformations and segmental overgrowth consistent with a clinical diagnosis of CLOVES syndrome; he passed away at 29 days of life. We discuss the complexities and limitations of genetic testing for somatic mosaic mutations in the prenatal period and highlight the potential need for multiple approaches to arrive at a molecular diagnosis. © 2014 Wiley Periodicals, Inc.

Uncovering the Genetic Etiology of Inherited Bone Marrow Failure Syndromes Using a Custom-Designed Next-Generation Sequencing Panel.

Inherited bone marrow failure syndromes (IBMFS) are a group of heterogeneous disorders that account for ∼30% of pediatric cases of bone marrow failure and are often associated with developmental abnormalities and cancer predisposition. This article reports the laboratory validation and clinical utility of a large-scale, custom-designed next-generation sequencing panel, Children's Hospital of Philadelphia (CHOP) IBMFS panel, for the diagnosis of IBMFS in a cohort of pediatric patients. This panel demonstrated excellent analytic accuracy, with 100% sensitivity, ≥99.99% specificity, and 100% reproducibility on validation samples. In 269 patients with suspected IBMFS, this next-generation sequencing panel was used for identifying single-nucleotide variants, small insertions/deletions, and copy number variations in mosaic or nonmosaic status. Sixty-one pathogenic/likely pathogenic variants (54 single-nucleotide variants/insertions/deletions and 7 copy number variations) and 24 hypomorphic variants were identified, resulting in the molecular diagnosis of IBMFS in 21 cases (7.8%) and exclusion of IBMFS with a diagnosis of a blood disorder in 10 cases (3.7%). Secondary findings, including evidence of early hematologic malignancies and other hereditary cancer-predisposition syndromes, were observed in 9 cases (3.3%). The CHOP IBMFS panel was highly sensitive and specific, with a significant increase in the diagnostic yield of IBMFS. These findings suggest that next-generation sequencing-based panel testing should be a part of routine diagnostics in patients with suspected IBMFS.

Tumor necrosis factor receptor 1 functions as a tumor suppressor.

Tumor necrosis factor (TNF) is a key player in inflammatory bowel disease and has been variably associated with carcinogenesis, but details of the cross talk between inflammatory and tumorigenic pathways remain incompletely understood. It has been shown that, in C57BL/6 mice, signaling via TNF receptor 1 (TNFR1) is protective from injury and inflammation in experimental colitis. Therefore, we hypothesized that loss of TNFR1 signaling would confer increased risk of developing colitis-associated carcinoma. Using three models of murine tumorigenesis based on repeated bouts of inflammation or systemic tumor initiator, we sought to determine the roles of TNF and TNFR1 with regard to neoplastic transformation in the colon in wild-type (WT), TNFR1 knockout (R1KO), and TNF knockout (TNFKO) mice. We found R1KO animals to have more severe disease, as defined by weight loss, hematochezia, and histology. TNFKO mice demonstrated less weight loss but were consistently smaller, and rates and duration of hematochezia were comparable to WT mice. Histological inflammation scores were higher and neoplastic lesions occurred more frequently and earlier in R1KO mice. Apoptosis is not affected in R1KO mice although epithelial proliferation following injury is more ardent even before tumorigenesis is apparent. Lastly, there is earlier and more intense expression of activated ß-catenin in these mice, implying a connection between TNFR1 and Wnt signaling. Taken together, these findings show that in the context of colitis-associated carcinogenesis TNFR1 functions as a tumor suppressor, exerting this effect not via apoptosis but by modulating activation of ß-catenin and controlling epithelial proliferation.

Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers.

Gene fusions are one of the most common genomic alterations in pediatric cancer. Many fusions encode oncogenic drivers and play important roles in cancer diagnosis, risk stratification, and treatment selection. We report the development and clinical validation of a large custom-designed RNA sequencing panel, CHOP Fusion panel, using anchored multiplex PCR technology. The panel interrogates 106 cancer genes known to be involved in nearly 600 different fusions reported in hematological malignancies and solid tumors. The panel works well with different types of samples, including formalin-fixed, paraffin-embedded samples. The panel demonstrated excellent analytic accuracy, with 100% sensitivity and specificity on 60 pediatric tumor validation samples. In addition to identifying all known fusions in the validation samples, three unrecognized, yet clinically significant, fusions were also detected. A total of 276 clinical cases were analyzed after the validation, and 51 different fusions were identified in 104 cases. Of these fusions, 16 were not previously reported at the time of discovery. These fusions provided genomic information useful for clinical management. Our experience demonstrates that CHOP Fusion panel can detect the vast majority of known and certain novel clinically relevant fusion genes in pediatric cancers accurately, efficiently, and cost-effectively; and the panel provides an excellent tool for new fusion gene discovery.

Clinical utility of custom-designed NGS panel testing in pediatric tumors.

BACKGROUND: Somatic genetic testing is rapidly becoming the standard of care in many adult and pediatric cancers. Previously, the standard approach was single-gene or focused multigene testing, but many centers have moved towards broad-based next-generation sequencing (NGS) panels. Here, we report the laboratory validation and clinical utility of a large cohort of clinical NGS somatic sequencing results in diagnosis, prognosis, and treatment of a wide range of pediatric cancers. METHODS: Subjects were accrued retrospectively at a single pediatric quaternary-care hospital. Sequence analyses were performed on 367 pediatric cancer samples using custom-designed NGS panels over a 15-month period. Cases were profiled for mutations, copy number variations, and fusions identified through sequencing, and their clinical impact on diagnosis, prognosis, and therapy was assessed. RESULTS: NGS panel testing was incorporated meaningfully into clinical care in 88.7% of leukemia/lymphomas, 90.6% of central nervous system (CNS) tumors, and 62.6% of non-CNS solid tumors included in this cohort. A change in diagnosis as a result of testing occurred in 3.3% of cases. Additionally, 19.4% of all patients had variants requiring further evaluation for potential germline alteration. CONCLUSIONS: Use of somatic NGS panel testing resulted in a significant impact on clinical care, including diagnosis, prognosis, and treatment planning in 78.7% of pediatric patients tested in our institution. Somatic NGS tumor testing should be implemented as part of the routine diagnostic workup of newly diagnosed and relapsed pediatric cancer patients.

The importance of and a method for including transfection efficiency into real-time PCR data analyses.

The polymerase chain reaction (PCR) is widely used to ascertain absolute or relative changes in the expression levels of specific genes as a function of cell type or in response to changes in environmental stimuli. Real-time PCR is an advance which allows for the analysis of gene expression over a wide range of initial cDNA concentrations, where the cDNA is the product of reverse transcriptase reactions applied to RNA samples. With the advent and advances in gene delivery technologies, it is now common for the cellular responses under scrutiny to be initiated via the expression of an exogenously delivered gene. When transfection (or transduction) is a part of the procedure used to prepare cell samples for real-time PCR, it is necessary to take the efficiency of gene delivery into account. Here a robust mathematical model for such analyses is derived, and validated with theoretical and experimental support. Comparison to existing analysis methods is presented to demonstrate the high significance of noting transfection, loading, and primer PCR efficiencies when processing PCR data.

Overgrowth Syndromes Caused by Somatic Variants in the Phosphatidylinositol 3-Kinase/AKT/Mammalian Target of Rapamycin Pathway.

Somatic variants have been well described in tumorigenesis; however, they are only recently appreciated in other human disorders, such as mosaic overgrowth syndromes. Although overgrowth is a manifestation in many genetic syndromes, not all overgrowth syndromes are inherited. Mosaic somatic variants have been lately described in several overgrowth disorders, such as Proteus syndrome, CLOVES (congenital, lipomatous, overgrowth, vascular malformations, epidermal nevi, and spinal/skeletal anomalies and/or scoliosis) syndrome, and megalencephalyepolymicrogyria-polydactyly-hydrocephalus syndrome. These syndromes are caused by somatic variants in the genes associated with the phosphatidylinositol 3-kinase/AKT/mammalian target of rapamycin pathway, resulting in a spectrum of overgrowth syndromes with overlapping features that could be difficult to distinguish based on phenotypic presentations alone. In addition, Sanger sequencing is ineffective for the detection of a causal variant because of the mosaic nature of these variants, whereas targeted next-generation sequencing technology offers a deeper sequencing coverage and allows the detection of low-level mosaicism. Recent studies have shown that the causal variants are only present in the affected tissues in most cases, and can be enriched by in vitro tissue culture. In this review, we describe several mosaic somatic overgrowth syndromes caused by variants in genes of the phosphatidylinositol 3-kinase/AKT/mammalian target of rapamycin signaling pathway, their phenotypic and molecular spectrum, and the clinical utility of next-generation sequencing technology in the diagnosis of these disorders.

Molecular Diagnosis of Mosaic Overgrowth Syndromes Using a Custom-Designed Next-Generation Sequencing Panel.

Recent studies have discovered a group of overgrowth syndromes, such as congenital lipomatous overgrowth with vascular, epidermal, and skeletal anomalies (CLOVES) syndrome, Proteus syndrome, and megalencephaly-capillary malformation-polymicrogyria (MCAP) syndrome, are caused by somatic activating variants in genes involved in the phosphatidylinositol 3-kinase/AKT/mechanistic target of rapamycin pathway. Because of the low-abundance nature of these variants, Sanger sequencing often yields negative results. We have developed and validated a next-generation sequencing (NGS) panel that targets all known variants associated with these syndromes. Fifty cases, including two prenatal cases, were tested using the panel. A pathogenic variant in the PIK3CA, PIK3R2, or AKT1 gene was identified in 28 of the 50 cases with the variant allele frequencies ranging from 1.0% to 49.2%. These variants were only present in the affected tissues in most of the cases, demonstrating a causal role in the development of these diseases. In vitro cell culture showed significant enrichment of the cells harboring variant alleles, suggesting that these variants render growth advantages to mutant cells. Phenotype-genotype correlation analysis showed PIK3CA mutation hotspots at residues E542, E545, and H1047 are often associated with CLOVES syndrome, whereas PIK3CA G914R is preferentially related to MCAP. We thus demonstrate that NGS technology is highly sensitive for detecting low-level mosaicism and can facilitate clinical diagnosis of mosaic overgrowth syndromes in both prenatal and postnatal settings.

Occurrence of deoxynivalenol in wheat, Hebei Province, China.

Analysis of deoxynivalenol (DON) and its metabolites 3-acetyl and 15-acetyldeoxynivalenol (3-ADON and 15-ADON) in wheat flour samples by liquid chromatography-tandem mass spectrometry (LC/MS/MS) during 2011-2013 was conducted. [(13)C15]-DON was used as the internal standard to accomplish as accurate as possible quantitation. Of all wheat samples (n=672), 91.5% were positive for DON, at levels ranging from 2.4 to 1130 µg/kg, with a median value of 154 µg/kg. The DON derivatives (3-Ac-DON, 15-Ac-DON) were far less frequently found and at lower levels than DON. The probable daily intakes (PDI) of DON (0.49 in 2011; 0.86 in 2012; 0.56 in 2013, expressed as µg/kg body weight/day) were all within the PDI of 1.0 µg/kg of bw/day for DON set by Scientific Committee for Food (SCF) in 2002. Still, persistent monitoring of DON is important.

Survey of 11 mycotoxins in wheat flour in Hebei province, China.

A survey of 11 mycotoxins in 348 wheat flour samples marketed in Hebei province of China were analysed by liquid chromatography-tandem mass spectrometry, was carried out. The selected mycotoxins consisted of four aflatoxins (AFs: AFB1, AFB2, AFG1 and AFG2) and seven Fusarium toxins, i.e. deoxynivalenol (DON), nivalenol, 3-acetyldeoxynivalenol and 15-acetyldeoxynivalenol, zearalenone, Fusarenon-X and deoxynivalenol-3-glucoside. Results indicated that most of the wheat samples analysed were contaminated with mycotoxins. Wheat was most susceptible to DON (91.4% contamination), with a mean level of 240 µg kg(-1). On average the probable daily intake (PDI, expressed as µg kg(-1) body weight day(-1)) of mycotoxins was within the provisional maximum tolerable daily intake (PMTDI, 2.0 µg kg(-1) of body weight day(-1)) as set by the Joint FAO/WHO Expert Committee on Food Additives. Nevertheless, exposure assessment revealed that the maximum PDI of mycotoxins was 4.06 µg kg(-1) body weight day(-1), which was twice the PMTDI value. Thus, consistent monitoring is recommended, as to keep the contamination level under control.

2-acetyl-4-tetrahydroxybutylimidazole and 4-methylimidazole in caramel colours, vinegar and beverages in China.

A survey of 2-acetyl-4-tetrahydroxybutylimidazole (THI) and 4-methylimidazole (4-MeI) concentrations in caramel colours, vinegar and beverages from the Chinese market were performed by ultrahigh-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). In total, 117 samples, 78 caramel colour samples, 23 vinegar samples and 16 beverage samples, were investigated. The results indicated that 4-MeI was found in all samples. THI was found in a part of the samples and also the level range was lower compared to 4-MeI. In caramel colour samples, the concentration level range of THI was 1.0-74.3 mg/kg and of 4-MeI was 1.5-1291.8 mg/kg. In vinegar samples, the concentration level range of THI was 13.3-119.2 µg/L and for 4-MeI 111.2-2077.8 µg/L. In beverage samples, THI was only found in two samples and the concentration level range of 4-MeI was 10.8-307.1 µg/L. THI and 4-MeI levels in vinegar and beverages were rather low compared with those in caramel colour samples. These observations can be helpful for evaluating individual exposure to THI and 4-MeI from caramel colours, vinegar and beverages in China.

Changes in DNA base sequences in the mutant of Arabidopsis thaliana induced by low-energy N(+) implantation.

To reveal the mutation effect of low-energy ion implantation on Ambidopsis thaliana in vivo, T80II, a stable dwarf mutant, derived from the seeds irradiated by 30 keV N(+) with the dose of 80 X 10(15) ions/cm(2) was used for Random Amplified Polymorphic DNA (RAPD) and base sequence analysis. The results indicated that among total 397 RAPD bands observed, 52 bands in T80II were different from those of wild type showing a variation frequency 13.1%. In comparison with the sequences of A. thaliana in GenBank, the RAPD fragments in T80II were changed greatly in base sequences with an average rate of one base change per 16.8 bases. The types of base changes included base transition, transversion, deletion and insertion. Among the 275 base changes detected, single base substitutions (97.09%) occurred more frequently than base deletions and insertions (2.91%). And the frequency of base transitions (66.55%) was higher than that of base transversions (30.55%). Adenine, thymine, guanine or cytosine could be replaced by any of other three bases in cloned DNA fragments in T80II. It seems that thymine was more sensitive to the irradiation than other bases. The flanking sequences of the base changes in RAPD fragments in T80II were analyzed and the mutational "hotspot" induced by low-energy ion implantation was discussed.

[Cloning and characterization of two MADS box genes from peach (Prunus persica)].

With the aim of finding genes involved in the floral transition of Prunus species (Prunus sp.), the EST (expressed sequence tags) sequences were extracted from the public databases. Eight MADS box genes' cDNAs were obtained. Two of them, PpMADS4 and PpMADS6 (The accession numbers in GenBank are AY705972 and AY705973), were cloned from peach (Prunus persica). The full length cDNA of PpMADS4 is 850 bp long. It contains an open reading frame of 732 bp, coding for a polypeptide of 243 amino acids. The full length cDNA of PpMADS6 is 1,190 bp long. It contains an open reading frame of 768 bp coding for a polypeptide of 256 amino acids. PpMADS4 closely resembles the Arabidopsis AGAMOUS gene. It is an AGAMOUS-like C class MADS box gene, and it expresses in petal, carpel, fruit and nutlet as demonstrated by RT-PCR analysis. PpMADS6 is likely to be the peach orthologue of the Petunia PFG genes and it is an A class MADS box gene. It has been shown with RT-PCR that it expresses in leaf, sepal, petal, carpel and fruit. It may be involved in the transition from the juvenile to the adult stage.

Clinical application of amplicon-based next-generation sequencing in cancer.

Next-generation sequencing (NGS) technology has revolutionized genomic research by decreasing the cost of sequencing while increasing the throughput. The focus now is on potential clinical applications of NGS technology for diagnostics and therapeutics. Clinical applications of NGS in cancer can detect clinically actionable genetic/genomic alterations that are critical for cancer care. These alterations can be of diagnostic, prognostic, or therapeutic significance. In certain cancers, patient risk and prognosis can be predicted based on the mutation profile identified by NGS. Many targeted therapies have been developed for cancer patients who bear specific mutations; however, choosing the right NGS technique for the appropriate clinical application can be challenging, especially in clinical oncology, where the material for NGS tests is often limited and the turnaround time (TAT) for cancer tests is constrained to a few days. Currently, amplicon-based NGS approaches have emerged as the best fit for clinical oncology. In this review, we focus on amplicon-based library preparation, sequencing, sequence data alignment and annotation, and post-analytic interpretation and reporting.

Determination of aflatoxins in edible oil from markets in Hebei Province of China by liquid chromatography-tandem mass spectrometry.

Analysis of aflatoxin B1 (AFB1), B2 (AFB2), G1 (AFG1) and G2 (AFG2) in 76 edible oil samples (peanut oil, soybean oil, corn embryo oil and blended oil) was performed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The oils were sampled from three areas (Shijiazhuang, Baoding and Tangshan) of Hebei Province of China. AFB1 was detected in 22 samples representing 28.9%, followed by AFB2 (7.89%) and AFG1 (3.95%), while no AFG2 contamination was detected in any samples. AFB1 levels in oil samples ranged 0.14-2.72 µg kg(-1) and AFB2 ranged 0.15-0.36 µg kg(-1), while lower levels of 0.01-0.02 µg kg(-1) for AFG1 were recorded. The paper is part of an on-going investigation of aflatoxin contamination in Chinese edible oils.