Genomic characterization of a PPP1CB-ALK fusion with fusion gene amplification in a congenital glioblastoma

ALK (Anaplastic lymphoma kinase) fusion proteins are oncogenic and have been seen in various tumors. PPP1CB-ALK fusions are rare but have been reported in a few patients with low- or high-grade gliomas. However, little is known regarding the mechanism of fusion formation and genomic break points of this fusion. We performed genomic characterization of a PPP1CB-ALK fusion with fusion gene amplification in a congenital glioblastoma. The PPP1CB-ALK consists of exons 1-5 of PPP1CB and exons 20-29 of ALK. The genomic translocation breakpoints were determined by real-time quantitative PCR (RT-qPCR) and Sanger sequencing of genomic DNA. Next generation sequencing, RT-qPCR and fluorescence in situ hybridization analyses demonstrated PPP1CB-ALK amplification. Copy number analyses of genes between PPP1CB and ALK using RT-qPCR suggest that the PPP1CB-ALK is likely the result of local chromothripsis followed by episomal amplification. Transcriptome sequencing demonstrated high-level SOX2 expression and predicted WNT/β-catenin pathway activation, suggesting possible therapeutic approaches.

The spectrum of rare central nervous system (CNS) tumors with EWSR1-non-ETS fusions: experience from three pediatric institutions with review of the literature

The group of CNS mesenchymal (non‐meningothelial) and primary glial/neuronal tumors in association with EWSR1‐non‐ETS rearrangements comprises a growing spectrum of entities, mostly reported in isolation with incomplete molecular profiling. Archival files from three pediatric institutions were queried for unusual cases of pediatric (≤21 years) CNS EWSR1‐rearranged tumors confirmed by at least one molecular technique. Extra‐axial tumors and cases with a diagnosis of Ewing sarcoma (EWSR1‐ETS family fusions) were excluded. Additional studies, including anchored multiplex‐PCR with next‐generation sequencing and DNA methylation profiling, were performed as needed to determine fusion partner status and brain tumor methylation class, respectively. Five cases (median 17 years) were identified (M:F of 3:2). Location was parenchymal (n = 3) and undetermined (n = 2) with topographic distributions including posterior fossa (n = 1), frontal (n = 1), temporal (n = 1), parietal (n = 1) and occipital (n = 1) lobes. Final designation with fusion findings included desmoplastic small round cell tumor (EWSR1‐WT1; n = 1) and tumors of uncertain histogenesis (EWSR1‐CREM, n = 1; EWSR1‐CREB1, n = 1; EWSR1‐PLAGL1, n = 1; and EWSR1‐PATZ1, n = 1). Tumors showed a wide spectrum of morphology and biologic behavior. For EWSR1‐CREM, EWSR1‐PLAGL1 and EWSR1‐PATZ1 tumors, no significant methylation scores were reached in the known brain tumor classes. Available outcome (4/5) was reported as favorable (n = 2) and unfavorable (n = 2) with a median follow‐up of 30 months. In conclusion, we describe five primary EWSR1‐non‐ETS fused CNS tumors exhibiting morphologic and biologic heterogeneity and we highlight the clinical importance of determining specific fusion partners to improve diagnostic accuracy, treatment and monitoring. Larger prospective clinicopathological and molecular studies are needed to determine the prognostic implications of histotypes, anatomical location, fusion partners, breakpoints and methylation profiles in patients with these rare tumors.

A germline PALB2 pathogenic variant identified in a pediatric high-grade glioma

PALB2 (partner and localizer of BRCA2) gene encodes a protein that colocalizes with BRCA2 in nuclear foci and likely permits the stable intranuclear localization and accumulation of BRCA2. PALB2 plays a critical role in maintaining genome integrity through its role in the Fanconi anemia and homologous recombination DNA repair pathways. It has a known loss-of-function disease mechanism. Biallelic PALB2 pathogenic variants have been described in autosomal recessive Fanconi anemia. Heterozygous pathogenic variants in PALB2 are associated with increased risk for female and male breast cancer and pancreatic cancer (Science 324: 217; Cancer Res 71: 2222–2229; N Engl J Med 371: 497–506). Heterozygous germline PALB2 mutations have also been observed in patients with medulloblastoma (Lancet Oncol 19: 785–798). However, PALB2-related cancer predisposition to high-grade gliomas has not been reported. Here we report a germline PALB2 pathogenic variant (c.509_510delGA, p.Arg170Ilefs*14, NM_024675.3) found in a pediatric patient with high-grade glioma. This variant was first identified by tumor sequencing using the Children's Hospital of Philadelphia (CHOP) Comprehensive Solid Tumor Panel and then confirmed to be a germline change using the CHOP Comprehensive Hereditary Cancer Panel on DNA from a blood sample of this patient. Parental studies showed that this variant was paternally inherited. Further studies are needed to illustrate if pathogenic variants in PALB2 convey increased risk to developing brain tumor. This case also highlights the potential of identifying germline mutation through tumor sequencing.

A Rare TP53 Mutation Predominant in Ashkenazi Jews Confers Risk of Multiple Cancers

Germline mutations in TP53 cause a rare high penetrance cancer syndrome, Li-Fraumeni syndrome (LFS). Here, we identified a rare TP53 tetramerization domain missense mutation, c.1000G>C;p.G334R, in a family with multiple late-onset LFS-spectrum cancers. Twenty additional c.1000G>C probands and one c.1000G>A proband were identified, and available tumors showed biallelic somatic inactivation of TP53. The majority of families were of Ashkenazi Jewish descent, and the TP53 c.1000G>C allele was found on a commonly inherited chromosome 17p13.1 haplotype. Transient transfection of the p.G334R allele conferred a mild defect in colony suppression assays. Lymphoblastoid cell lines from the index family in comparison with TP53 normal lines showed that although classical p53 target gene activation was maintained, a subset of p53 target genes (including PCLO, PLTP, PLXNB3, and LCN15) showed defective transactivation when treated with Nutlin-3a. Structural analysis demonstrated thermal instability of the G334R-mutant tetramer, and the G334R-mutant protein showed increased preponderance of mutant conformation. Clinical case review in comparison with classic LFS cohorts demonstrated similar rates of pediatric adrenocortical tumors and other LFS component cancers, but the latter at significantly later ages of onset. Our data show that TP53 c.1000G>C;p.G334R is found predominantly in Ashkenazi Jewish individuals, causes a mild defect in p53 function, and leads to low penetrance LFS. SIGNIFICANCE: TP53 c.1000C>G;p.G334R is a pathogenic, Ashkenazi Jewish-predominant mutation associated with a familial multiple cancer syndrome in which carriers should undergo screening and preventive measures to reduce cancer risk.

[Feasibility and efficacy of partial superficial parotidectomy with V-shaped incision]

Objective: To evaluate the feasibility and efficacy of partial superficial parotidectomy with V-shaped incision by comparing with the Blair incision and hairline N-shaped incision. Methods: From January 2015 to January 2016, 60 patients (47 males and 13 females, with an age range of 25- 63 years) required for superficial partial parotid gland resection were randomly divided into three groups: V-shaped incision (VI) group, Blair incision (BI) group and hairline N-shaped incision (NI) group, with 20 cases in each group.Intraoperative, postoperative and follow-up indexes were compared between three groups. Operative time and drainage volume in the surgery of tumors at different sites in VI group were compared. SPSS18.0 software was used for statistic analysis. Results: There were no statistically significant differences among the three groups in operative time, drainage volume, postoperative hospital stay, periauricular numbness, fistulas, pain score, facial palsy, and scar score at the 3rd month after surgery (P>0.05). For appearance satisfaction score at the 6th month after surgery, VI group was better than BI group or NI group, with significant differences(VI group vs. BI group: 9.00[8.00, 9.00] vs. 5.00[4.00, 5.25], χ(2)=6.629, P<0.001; VI group vs. NI group: 9.00[8.00, 9.00] vs. 7.00[6.00, 8.00], χ(2)=2.942, P=0.010; BI group vs. NI group: 5.00[4.00, 5.25] vs. 7.00[6.00, 8.00], χ(2)=-3.687, P=0.001). For tumors located in the front, upper and middle of parotid gland, there were no statistically significant differences in operative time and drainage volume between the three groups (P>0.05). For tumors located at the lower part of parotid gland, the difference in operative time between the three groups was statistically significant (F=7.278, P=0.01). With pairwise comparison, operative time in VI group was longer than that in BI group or NI group, but there was no significant difference between BI group and NI group (VI group vs. BI group: (181.00±22.89) min vs. (132.50±9.01) min, t=3.694, P=0.004; VI group vs. NI group:(181.00±22.89) min vs. (149.00±15.94) min, t=2.585, P=0.025; BIgroup vs. NI group, (132.50±9.01) min vs. (149.00±15.94) min, t=1.257, P=0.235). For tumors located at the lower part of parotid gland, the differences in intraoperative drainage volume were not statistically significant between three groups (P>0.05). There were no statistically significant differences in operative time and drainage volume in the surgery of tumors at different sites in VI group (P>0.05). Conclusions: By use of V-shaped incision for the surgery of benign parotid gland tumors, the operation time of tumors located only in the lower part of the parotid gland will be prolonged. For tumors in different sites without increasing surgical complications, this modality can get good cosmetic effect.

Evolution of histomorphologic, cytogenetic, and genetic abnormalities in an untreated patient with MIRAGE syndrome

Gain of function variants in SAMD9 cause MIRAGE syndrome, a rare Mendelian disorder that results in myeloid dysplastic syndrome (MDS), poor immune response, restricted growth, adrenal insufficiency, ambiguous genitalia, feeding difficulties and most often significantly reduced lifespan. In this study, we describe histomorphologic and genetic changes occurring in serial bone marrow measurements in a patient with MIRAGE syndrome and untreated MDS of 9 years. Histomorphological analysis during childhood showed progressive hypocellularity with erythroid and megakaryocytic dysplasia and cytogenetic testing demonstrated monosomy 7. Serial leukemia gene panel testing performed over a seven year period revealed multiple pre-leukemic clones arising at age 7 years followed by sequential mutational events in ETV6 and RUNX1 driving acute myeloid leukemia (AML) at age 9. Comprehensive genotype-phenotype analysis with 28 previously reported patients found the presence of MDS did not impact overall survival, but in silico variant pathogenicity prediction scores for SAMD9 distinguished patients with poor prognosis. Overall, our analysis shows progression of MDS to AML can be monitored by following mutation evolution in leukemia related genes in patients with MIRAGE syndrome, and specific SAMD9 mutations likely influence disease severity and overall survival.

Clinical significance of serial tumor next generation sequencing (NGS) in 155 pediatric cancer patients

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Background: Molecular profiling using NGS technology is critical for tumor diagnosis, risk stratification, and treatment selection. There are limited data in childhood cancers regarding evolution of genomic changes under the selective pressure of chemoradiotherapy. Here we report on serial testing of hematologic and solid pediatric tumor specimens across the spectrum of diagnosis, during treatment and disease relapse. Methods: Since 2016, 2,144 somatic NGS assays from 1,727 unique cancer patients were performed using the Comprehensive Hematological Malignancy Panel (CHMP) or the Comprehensive Solid Tumor Panel (CSTP). Serial tumor analysis was performed on 155 patients. All tumors were profiled for SNVs/indels, copy number alterations (CNAs), and fusions. The clinical impact on diagnosis, prognosis, and therapy was assessed. Results: 85 and 70 patients were tested with CHMP and CSTP, respectively. 86.5% (134/155) of patients underwent 1 subsequent genetic testing, while 13.5% (21/155) were serially tested for 3 - 6 times. Relapsed or therapy-refractory tumor was the most common indication for repeat CHMP and CSTP analysis of tumor genomics (64.5%, 100/155), primarily to survey for new targetable cancer driver mutations. The second most common reason for serial testing with CHMP was to monitor clonal evolution for patients with bone marrow failure syndromes and/or myelodysplastic syndromes, which resulted in a new cancer diagnosis in 14.6% (6/41) patients. For CSTP, the second most common reason for serial testing was to test a different part of the same tumor for tumors with histologic and/or radiographic heterogeneity (27.1%, 19/70). Of all patients with serial testing, 70 had at least one clinically significant new SNV/indel, 44 had distinct CNAs, and 4 had new clinically actionable fusions. Overall, clinically significant new results were detected in 81 (52.3%) patients, including 53 patients with new clonal changes indicating disease evolution, 31 of diagnostic significance, 9 of prognostic significance, and 8 suggesting new treatment options. Conclusions: Taken together, these data highlight the clinical importance of serial testing of pediatric tumors for potential biomarkers that may impact patients’ care at various time points across the spectrum of their diseases.

Whole genome SNP arrays for best practice for detection of diagnostic, prognostic and therapy related copy number changes and copy neutral-loss of heterozygosity across solid tumors and hematologic malignancies

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Background: High resolution single nucleotide polymorphism (SNP) chromosomal microarrays (CMA) detect copy number changes and copy neutral-loss of heterozygosity (CN-LOH) across the entire genome, currently providing the best assessment for these types of genomic variants. Chromosomal microarrays are first tier tests utilized in the postnatal detection of microdeletions, microduplications and uniparental disomy/regions of homozygosity in constitutional disorders involving congenital abnormalities, developmental delay and intellectual disability. Methods: In the oncology setting, aberrations detected may be diagnostic, prognostic, and therapeutic. Because CMA assesses the entire genome and can readily detect aberrations as small as a single exon to as large as a whole chromosome, this is an important clinical tool to bridge the gap between low resolution of metaphase chromosome analysis and PCR-based short read sequencing-based assays. Results: No single genomic technique (metaphase chromosome analysis, FISH, CMA or Next Generation Sequencing, including large targeted gene panels) has the ability to detect all relevant information. Therefore, CMA should be considered an important clinical tool for solid and liquid tumors. Across a wide variety of solid tumors, whole genome assessment (including oncogene amplification, tumor suppressor loss, and copy number burden) leads not only to possible therapy targets but also to opportunities for participation in active clinical trials. Recently, the Cancer Genomics Consortium has published evidenced-based reviews on the clinical utility of CMA for copy number and CN-LOH assessment in a variety of hematologic malignancies, and similar papers in solid tumors are in review. Recognizing the growing evidence for CMA, the American Medical Association (AMA) CPT editorial board recently created a new Tier 1 test for cytogenomic arrays in neoplasia, and Centers for Medicare and Medicaid Services (CMS) approved crosswalking the price of the new code to the well-established constitutional cytogenomic array CPT code. Conclusions: For this presentation, examples of diagnostic, prognostic, and therapeutic utility and inclusion in clinical trials across many hematologic and solid tumor neoplasms will be presented to demonstrate the efficacy, cost effectiveness and sensitivity of whole genome assessment of copy number and copy neutral loss of heterozygosity

[Evaluation of human milk feeding in hospitalized very low and extremely low birth weight infants]

Objective: To investigate the current situation of human milk (HM) feeding in hospitalized very low and extremely low birth weight infants. Methods: The study retrospectively extracted the data of 601 infants with birth weight <1 500 g, and admitted within 24 hours after birth to the Neonatal Intensive Care Unit of Nanjing Maternity and Child Health Care Hospital from January 2016 to December 2018. The infants were grouped into exclusive mother's-own-milk (MOM) group, donor human milk (DHM) group (partial or none MOM), and mixed (HM and formula) feeding group according to the feeding strategy. Qualitative and quantitative variables in the three groups were compared with One-way ANOVA, Kruskal-Wallis test, Chi-square test or Fisher exact test. Kappa and McNemar test were used for consistency testing. Results: Among the 601 infants (309 boys and 292 girls), 6 (1.0%) infants had never been fed with MOM. The gestational age and birth weight were (29.3±1.9) weeks and 1 260(1 115, 1 400) g in 601 infants. A total of 8 (1.3%) infants were grouped into MOM group, 542 (90.2%) were grouped into DHM group, and 51 (8.5%) were grouped into mixed feeding group. The percentage of enteral feedings with MOM in the stage of hospitalization 1-7 d, 8-14 d and 15-28 d were 73.6% (42.9%, 86.7%), 97.5% (78.6%, 100.0%) and 99.3% (93.0%, 100.0%), respectively (H=414.95, P<0.01), and the pairwise comparison suggested that the stage of hospitalization 1-7 d was the lowest (adjusted both P<0.05). The average weight adjusted daily dose of MOM were 9.7 (4.3, 18.2), 59.1 (26.5, 93.5) and 116.0 (60.3, 142.6) ml/(kg·d) in the stage of hospitalization 1-7 d, 8-14 d and 15-28 d, respectively (H=759.75, P<0.01), and the pairwise comparison suggested that the stage of hospitalization 1-7 d was the lowest (adjusted both P<0.05). The weight adjusted daily dose of MOM in exclusive MOM group, DHM and Mixed feeding group were 95.2 (40.0, 117.2), 82.9(53.6, 103.1) and 55.7 (16.6, 97.5) ml/(kg·d), respectively (H=10.78, P=0.005).Additionally, the percentage and weight adjusted daily dose of MOM showed a general consistency of 0.703 (P>0.05, Kappa=0.408). Conclusions: The rate of exclusive MOM feeding is low, especially during the first 7 days of hospitalization. The percentage of total enteral feedings with MOM and the average weight adjusted daily dose of MOM can well evaluate the situation of HM feeding during hospitalization quantitively.

Integrated Molecular and Clinical Analysis of 1,000 Pediatric Low-Grade Gliomas

Pediatric low-grade gliomas (pLGG) are frequently driven by genetic alterations in the RAS-mitogen-activated protein kinase (RAS/MAPK) pathway yet show unexplained variability in their clinical outcome. To address this, we characterized a cohort of >1,000 clinically annotated pLGG. Eighty-four percent of cases harbored a driver alteration, while those without an identified alteration also often exhibited upregulation of the RAS/MAPK pathway. pLGG could be broadly classified based on their alteration type. Rearrangement-driven tumors were diagnosed at a younger age, enriched for WHO grade I histology, infrequently progressed, and rarely resulted in death as compared with SNV-driven tumors. Further sub-classification of clinical-molecular correlates stratified pLGG into risk categories. These data highlight the biological and clinical differences between pLGG subtypes and opens avenues for future treatment refinement.

[Impact of maternal X chromosome aneuploidies on cell free DNA prenatal screening]

Objective: To investigate the impact of maternal X chromosome aneuploidies on cell free DNA (cf-DNA) prenatal screening. Methods: After genetic counseling, invasive prenatal diagnosis was provided for the 124 cases with high risk of sex chromosome aneuploidie (SCA) indicated by cf-DNA prenatal screening. For cases with discordant results of fetal prenatal diagnosis and cf-DNA prenatal screening, maternal leukocyte was collected for copy number variation sequencing (CNV-seq) to detect whether the maternal X chromosome was carrying variations. Results: Totally, 124 cases with high risks of SCA indicated by cf-DNA prenatal screening, 9 cases refused to take invasive prenatal diagnosis, while the remaining 115 cases received. Among the 115 cases, 41 cases received accordant results with cf-DNA prenatal screening while 74 cases discordant. Among the 74 cases with discordant results, 19 cases were indicated with maternal X chromosome variations by maternal leukocyte CNV-seq, which accounting for 25.7% (19/74) of the SCA false positive cases, and 15.3% (19/124) of all SCA cases. Conclusions: Pregnant women with X chromosome variations may affect the results of cf-DNA prenatal screening, resulting in false positive or false negative outcomes, it should be emphasized that the cf-DNA results may be affected by maternal X chromosome variations. In cases with discordant results of prenatal diagnosis and cf-DNA prenatal screening, maternal leukocyte CNV-seq is recommended to find the reasons of false positive or negative results. And cf-DNA prenatal screening is not recommended for pregnant women who are already known with X chromosome variations.

Copy number assessment in the genomic analysis of CNS neoplasia: An evidence-based review from the cancer genomics consortium (CGC) working group on primary CNS tumors

The period from the 1990s to the 2010s has witnessed a burgeoning sea change in the practice of surgical neuropathology due to the incorporation of genomic data into the assessment of a range of central nervous system (CNS) neoplasms. This change has since matured into the adoption of genomic information into the definition of several World Health Organization (WHO)-established diagnostic entities. The data needed to accomplish the modern diagnosis of CNS neoplasia includes DNA copy number aberrations that may be assessed through a variety of mechanisms. Through a review of the relevant literature and professional practice guidelines, here we provide a condensed and scored overview of the most critical DNA copy number aberrations to assess for a selection of primary CNS neoplasms.

[The association between the frequency of prenatal care in childbearing aged women and risk of small for gestational age among neonatal twins in Shaanxi Province]

Objective: To explore the association between the frequency of prenatal care in childbearing aged women and risk of small for gestational age (SGA) among neonatal twins in Shaanxi Province. Methods: From July to December 2013, a total of 30 027 childbearing aged women, who were pregnant from January 2010 to November 2013 and had definite outcomes, were selected from 30 districts (counties) of Shaanxi Province by using the multi-stage random sampling method. The questionnaires with a face-to-face survey method were used to retrospectively collect demographic information, pregnancy history, lifestyle during pregnancy, disease history, nutritional supplements, and health care during pregnancy. Information on the gestational age and birth weight of the newborn were obtained by consulting the medical certificate of birth and were registered as twin A and twin B by birth order. Finally, 356 childbearing aged women and their twin babies with complete data were included in the analysis. A generalized estimation equation model was used to analyze the association between the frequency of prenatal care and the risk of SGA among neonatal twins. Results: The age of childbearing aged women was (27.44±4.68) years old, of which 79.49% (283 women) were rural residents and 44.38% (158 women) had seven or more times prenatal care. The gestational age and birth weight were (37.64±2.51) weeks and (2 510±497) g, respectively. The prevalence of SGA was 51.40% (183/356) for twin A and 53.37% (190/356) for twin B, respectively. The prevalence of SGA was 44.30% (70/158) for twin A with seven or more times prenatal care and 42.41% (67/158) for twin B with seven or more times prenatal care, which was lower than that for twins with less than seven times prenatal care, respectively [57.07% (113/198) and 62.12% (123/198)] (P values were 0.017 and <0.001). The results of generalized estimation equation model suggested that compared to those with less than seven times prenatal care, after adjusting for parity, birth order, place of residence, maternal age, occupation, education, family wealth index, passive smoking, pregnancy-induced hypertension syndrome, folic acid, and iron supplement during perinatal period, and gender of the newborn, the OR (95%CI) of risk of SGA among childbearing aged women with seven or more times prenatal care was 0.60 (0.40-0.91). Conclusion: Seven or more times prenatal care could reduce the risk of SGA among neonatal twins in Shanxi Province.

Fermentation of flaxseed cake increases its nutritional value and utilization in ducklings

Flaxseed cake (FSC) is a potential alternative feed source in poultry. However, cyanogenetic glycosides limit its widespread use in feed. In this study, we optimized the parameters of fermentation by Aspergillus niger and Candida utilis and compared the growth performance, serum lipid parameters, and organ indexes of Cherry Valley duckling feed with unfermented FSC (UFSC) or fermented FSC (FFSC). A total of 420 one-day-old male Cherry Valley ducklings were randomly assigned into a 1 plus 2 × 3 factorial design including 2 different FSC resources (UFSC and FFSC) at 3 levels (50, 100, or 150 g/kg) for 3 wk. Each treatment group included 6 pens with 10 ducklings per pen. The hydrocyanic acid (HCN) level was reduced under the following conditions: 1:0.8 FSC:water (w:v), inoculum ratio of 1 mL:1 mL, 30°C, and 60 h. FFSC had higher crude protein (CP) and calcium (Ca) levels and lower HCN levels compared with UFSC (P < 0.05). There was no interactive effect between FSC sources and levels on growth performance. Final body weight (FBW), average daily feed intake (ADFI), and average daily gain (ADG) in UFSC groups and ADFI in FFSC groups decreased linearly with increasing FSC levels (P < 0.01). There were no differences in FBW, ADG, or feed:gain ratio (F/G) among FFSC groups, and all 7 FSC groups had no differences in the F/G ratio (P > 0.05). Dietary FSC supplementation decreased triglyceride (TG) (P < 0.01), total cholesterol (TC) (P < 0.01), high-density lipoprotein (HDL) (P = 0.01), and low-density lipoprotein (LDL) (P < 0.01). No interactive effect between FSC levels and sources was observed for serum TG, TC, HDL, or LDL. Ducklings fed FFSC had lower TG (P < 0.01), TC (P = 0.05), and LDL (P < 0.01) levels compared with ducklings fed UFSC. The 150 g/kg FFSC group had the lowest TG, TC, HDL, and LDL levels among all 7 groups. Flaxseed cake supplementation decreased the relative weight of the left breast, but FFSC increased the relative weight of the gizzard compared with UFSC. In conclusion, fermentation could increase the nutritional value and usage of FSC in ducklings.

Pediatric Somatic Tumor Sequencing Identifies Underlying Cancer Predisposition

PURPOSE

The diagnosis of cancer predisposition in pediatric patients with cancer is vital for treatment decisions, surveillance, and management of at-risk family members. Somatic tumor testing can identify potential underlying constitutional variants that confer increased cancer risk. Here, we report the characteristics of constitutional variants identified through tumor testing.

MATERIALS AND METHODS

Data were abstracted from medical record review of 1,023 patients who received inhouse somatic tumor testing over a 28-month period. Patients were identified for testing using referral criteria developed as a collaboration between genomic diagnostics, pathology, and oncology. Characteristics of patients who underwent constitutional testing, including family history and variant loss of heterozygosity, were tracked.

RESULTS

From 1,023 patients who underwent somatic tumor sequencing in a 28-month period, 210 variants were identified in 141 patients (13.8%) that were concerning for cancer predisposition syndromes requiring intervention. A total of 73 variants in 41 patients have undergone clinical confirmatory testing thus far. Of these, 26 variants were confirmed to be constitutionally present (35.6%). Among patients tested, 23 (56.1%) of 41 total patients were diagnosed with a cancer predisposition syndrome.

CONCLUSION

Our data demonstrate that more than one third of variants in tumor somatic sequencing that were concerning for underlying cancer predisposition were constitutionally confirmed. Overall, somatic tumor testing identified potential cancer predisposition syndromes in pediatric patients, and some would not have been identified on the basis of clinical history alone.

[Association between congenital heart disease and maternal disease in early pregnancy in women of childbearing age]

Objective: To investigate the relationship between maternal disease in early pregnancy of women of childbearing age and congenital heart disease of neonates. Methods: A cross-sectional design was used in this study and stratified multistage random sampling method was used. A questionnaire survey was conducted in the childbearing-aged women during 2010-2013 in Shaanxi province. Propensity score (PS) matched (1∶1) analysis was used to match participants with diseases to those without disease in early pregnancy. Through the control of the confounders step by step, a logistic regression model was established to evaluate the ORs of congenital heart disease according to the independent variable of maternal disease. Results: A total of 28 680 pairs of mothers and infants were included in this study, the proportion of the women with disease in early pregnancy was 20.25% (5 807). After PS matching, 5 436 pairs were matched. After adjusting all confounding factors, the multivariable logistic regression analysis results showed that maternal disease (OR=1.86, 95%CI: 1.23-2.81), especially cold (OR=2.19, 95%CI: 1.46-3.28), gynecological disease (OR=4.74, 95%CI: 2.03-11.09) and diabetes (OR=14.00, 95%CI: 1.64-119.21), in early pregnancy were the risk factors for congenital heart disease of neonate. Conclusion: In women of childbearing age, disease in early pregnancy, especially cold, gynecological disease and diabetes, can increase the risk of congenital heart disease in neonates.

Genomic Analysis of Dysembryoplastic Neuroepithelial Tumor Spectrum Reveals a Diversity of Molecular Alterations Dysregulating the MAPK and PI3K/mTOR Pathways

Dysembryoplastic neuroepithelial tumors (DNT) lacking key diagnostic criteria are challenging to diagnose and sometimes fall into the broader category of mixed neuronal-glial tumors (MNGT) or the recently described polymorphous low-grade neuroepithelial tumor of the young (PLNTY). We examined 41 patients with DNT, MNGT, or PLNTY for histologic features, genomic findings, and progression-free survival (PFS). Genomic analysis included sequence and copy number variants and RNA-sequencing. Classic DNT (n = 26) was compared with those with diffuse growth without cortical nodules (n = 15), 6 of which exhibited impressive CD34 staining classifying them as PLNTY. Genomic analysis was complete in 33, with sequence alterations recurrently identified in BRAF, FGFR1, NF1, and PDGFRA, as well as 7 fusion genes involving FGFR2, FGFR1, NTRK2, and BRAF. Genetic alterations did not distinguish between MNGTs, DNTs, or PLNTYs; however, FGFR1 alterations were confined to DNT, and PLNTYs contained BRAF V600E or FGFR2 fusion genes. Analysis of PFS showed no significant difference by histology or genetic alteration; however, numbers were small and follow-up time short. Further molecular characterization of a PLNTY-related gene fusion, FGFR2-CTNNA3, demonstrated oncogenic potential via MAPK/PI3K/mTOR pathway activation. Overall, DNT-MNGT spectrum tumors exhibit diverse genomic alterations, with more than half (19/33) leading to MAPK/PI3K pathway alterations.

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.

Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants

Background

Clinical laboratories implement a variety of measures to classify somatic sequence variants and identify clinically significant variants to facilitate the implementation of precision medicine. To standardize the interpretation process, the Association for Molecular Pathology (AMP), American Society of Clinical Oncology (ASCO), and College of American Pathologists (CAP) published guidelines for the interpretation and reporting of sequence variants in cancer in 2017. These guidelines classify somatic variants using a four-tiered system with ten criteria. Even with the standardized guidelines, assessing clinical impacts of somatic variants remains to be tedious. Additionally, manual implementation of the guidelines may vary among professionals and may lack reproducibility when the supporting evidence is not documented in a consistent manner.

Results

We developed a semi-automated tool called “Variant Interpretation for Cancer” (VIC) to accelerate the interpretation process and minimize individual biases. VIC takes pre-annotated files and automatically classifies sequence variants based on several criteria, with the ability for users to integrate additional evidence to optimize the interpretation on clinical impacts. We evaluated VIC using several publicly available databases and compared with several predictive software programs. We found that VIC is time-efficient and conservative in classifying somatic variants under default settings, especially for variants with strong and/or potential clinical significance. Additionally, we also tested VIC on two cancer-panel sequencing datasets to show its effectiveness in facilitating manual interpretation of somatic variants.

Conclusions

Although VIC cannot replace human reviewers, it will accelerate the interpretation process on somatic variants. VIC can also be customized by clinical laboratories to fit into their analytical pipelines to facilitate the laborious process of somatic variant interpretation. VIC is freely available at https://github.com/HGLab/VIC/.

Electronic supplementary material

The online version of this article (10.1186/s13073-019-0664-4) contains supplementary material, which is available to authorized users.

Effects of jugular infusions of isoleucine, leucine, methionine, threonine, and other amino acids on insulin and glucagon concentrations, mammalian target of rapamycin (mTOR) signaling, and lactational performance in goats

The supply and profile of absorbed AA may affect milk protein synthesis through hormonal changes and mammalian target of rapamycin (mTOR) signaling pathways; and Ile, Leu, Met, and Thr (ILMT) are the 4 AA that have been reported to have the greatest effect on mammary mTOR signaling. The extent to which ILMT and the other remaining AA (RAA) differ in their effects on milk protein synthesis needs to be systematically investigated. In this study, 5 lactating goats, averaging 120 ± 10 d in milk, fitted with jugular vein and carotid artery catheters, were fasted for 24 h, followed by intravenous infusions of a mixture containing AA and glucose for 8 h in a 5 × 5 Latin square design. The AA mixtures were formulated according to the profile of casein. The amounts of AA infused were calculated based on supplies of AA when metabolizable protein (MP) was at requirement (MR). Treatments were an infusate containing glucose without AA (NTAA); an infusate containing 3 × the MR of Ile, Leu, Met and Thr (3F0R); and infusates containing 3F0R plus 1, 2, or 3 × MR of RAA (3F1R, 3F2R, and 3F3R, respectively) according to amounts provided when fed to meet MP requirements for maintenance and lactation for each goat. Milk, arterial blood, and mammary tissue samples were collected immediately after halting the infusion. Relative to NTAA, supplementation of ILMT tended to increase milk protein production and plasma glucose concentrations, and increased milk and lactose production, but had no effects on production or content of milk fat. Graded supplementation of RAA tended to quadratically affect production of milk and lactose. Arterial glucose and glucagon concentrations decreased linearly, and plasma insulin concentrations decreased quadratically with increased RAA. Mammary p70-S6K1 phosphorylation was decreased by addition of ILMT compared with NTAA but increased linearly with increased RAA infusion. Furthermore, EIF4EBP1 gene expression was much lower for 3F-treated goats than for the NTAA treatment. Both MTOR and RPS6KB1 gene expressions were decreased quadratically with increased RAA supply. These results suggested that short-term milk protein yield tended to be increased by elevated ILMT availability, and this trend was not explained by variations in mammary mTOR signaling or pancreatic hormone secretions, whereas graded increase of RAA in combination with ILMT appeared to regulate the efficiency of conversion of glucose to lactose in a manner not involving milk protein production.

[Infiltration of tumor associated macrophages in multiple myeloma and its clinical significance]

目的

探讨肿瘤相关性巨噬细胞（TAM）在多发性骨髓瘤（MM）中的临床意义及其与肿瘤血管生成、免疫抑制的关系。

方法

以2015年8月至2017年6月就诊的70例MM患者为观察对象，以20例良性血液病（缺铁性贫血13例，巨幼细胞性贫血7例）患者为对照，采用免疫组化法检测骨髓标本中CD163、CD34、VEGF的表达，采用流式细胞术检测Treg细胞比例，采用ELISA法检测IL-10水平，结合临床特征进行分析。

结果

①70例患者中，男31例，女39例，中位年龄65（50~78）岁。MM患者组的TAM浸润密度、微血管密度（MVD）、VEGF表达水平、Treg细胞比例及IL-10水平均较对照组升高（P值均<0.05）。②在MM患者组中，疾病稳定组（15例）患者的上述指标均较初诊组（35例）和复发难治组（20例）低（P值均<0.05）；后两组差异无统计学意义（P值均>0.05）。③35例初诊MM患者中27例完成4个疗程治疗，有效组（15例）治疗后TAM浸润密度较治疗前明显下降，差异有统计学意义[（20.20±7.66）对（28.87±11.97）个/高倍，t=2.362，P=0.025]；无效组（12例）治疗前后差异无统计学意义[（42.00±13.76）对（48.25±13.59）个/高倍，t=1.119，P=0.275]。④硼替佐米方案治疗有效组患者（21例次）的TAM浸润密度较非硼替佐米方案治疗有效组（18例次）减低[（16.52±4.26）对（19.27±5.82）个/高倍，t=1.662，P=0.170]。⑤MM患者的TAM浸润密度与MVD、VEGF表达水平、Treg细胞比例及IL-10水平呈正相关（P值均<0.001）。

结论

骨髓微环境中浸润的TAM与MM发生、发展、疗效及治疗耐药有关，其作用机制可能与TAM促进肿瘤血管形成及抑制免疫反应有关。

Effects of milrinone on inflammatory response-related gene expressions in cultured rat cardiomyocytes

Congestive heart failure (CHF) is defined as a cardiac dysfunction leading to low cardiac output and inadequate tissue perfusion. Intravenous positive inotropes are used to increase myocardial contractility in hospitalized patients with advanced heart failure. Milrinone is a phosphodiesterase Ⅲ inhibitor and used most commonly for inotropic effect. The well-known PROMISE study investigated the effects of milrinone on mortality in patients with severe CHF, and concluded that long-term therapy with milrinone increased morbidity and mortality among patients with advanced CHF. Previous studies have suggested that phosphodiesterase inhibitors can have potential effects on inflammatory pathways. Hence, we hypothesized that milrinone may alter inflammatory gene expressions in cardiomyocytes, thus leading to adverse clinical outcomes. We used rat cardiomyocyte cell line H9C2 and studied the impact of exposing cardiomyocytes to milrinone (10 μmol/L) for 24 hours on inflammatory gene expressions. RNA extracted from cultured cardiomyocytes was used for whole rat genome gene expression assay (41,000 genes). The following changes in inflammatory response-related gene expressions were discovered. Genes with increased expressions included: THBS2 (+9.98), MMP2 (+3.47), DDIT3 (+2.39), and ADORA3 (+3.5). Genes with decreased expressions were: SPP1 (-5.28) and CD14 (-2.05). We found that the above mentioned gene expression changes seem to indicate that milrinone may hinder the inflammatory process which may potentially lead to adverse clinical outcomes. However, further in vivo and clinical investigations will be needed to illustrate the clinical relevance of these gene expression changes induced by milrinone.

SETD2 mutations in primary central nervous system tumors

Mutations in SETD2 are found in many tumors, including central nervous system (CNS) tumors. Previous work has shown these mutations occur specifically in high grade gliomas of the cerebral hemispheres in pediatric and young adult patients. We investigated SETD2 mutations in a cohort of approximately 640 CNS tumors via next generation sequencing; 23 mutations were detected across 19 primary CNS tumors. Mutations were found in a wide variety of tumors and locations at a broad range of allele frequencies. SETD2 mutations were seen in both low and high grade gliomas as well as non-glial tumors, and occurred in patients greater than 55 years of age, in addition to pediatric and young adult patients. High grade gliomas at first occurrence demonstrated either frameshift/truncating mutations or point mutations at high allele frequencies, whereas recurrent high grade gliomas frequently harbored subclones with point mutations in SETD2 at lower allele frequencies in the setting of higher mutational burdens. Comparison with the TCGA dataset demonstrated consistent findings. Finally, immunohistochemistry showed decreased staining for H3K36me3 in our cohort of SETD2 mutant tumors compared to wildtype controls. Our data further describe the spectrum of tumors in which SETD2 mutations are found and provide a context for interpretation of these mutations in the clinical setting.

[Association between congenital heart disease and medication taken during pregnancy among women of childbearing age]

Objective: To analyze the relationship between medication taken during pregnancy and congenital heart disease of the newborns. Methods: A large cross-sectional survey was conducted between August and November 2013. A questionnaire survey was conducted among the childbearing aged women, selected through multistage stratified random sampling in Shaanxi from 2010 to 2013. All of the childbearing aged women under study were in pregnancy and with definite pregnancy outcomes. Multivariable Poisson regression was conducted for data analyses. Results: A total of 28 680 cases were included in this study. The proportion of medication taken at any time during pregnancy was 16.0%, and the prevalence of congenital heart disease among the newborns was 67.9/10 000. After adjustment for factors as general demographic characteristic, history of heart disease and drug allergy and the situation of disease during pregnancy of these women, results from the multivariable Poisson regression showed that, factors as taking drugs (RR=1.95, 95%CI: 1.42- 2.68), cold medicine (RR=1.68, 95%CI: 1.07-2.64), antibiotics (RR=1.90, 95%CI: 1.25-2.90), salicylates (RR=5.01, 95%CI: 1.84-13.64) and antifungal drugs (RR=10.22, 95%CI: 3.25-32.19) during pregnancy were all related to congenital heart disease, and with the history of taking cold medicine (RR=1.90, 95%CI: 1.01-3.61), antibiotics (RR=2.18, 95%CI: 1.17-4.06), salicylates (RR=6.07, 95%CI: 1.45-25.41), antifungal drugs (RR=21.01, 95%CI: 4.17-105.87) and other drugs (RR=2.31, 95%CI: 1.19-4.47) during early pregnancy. These factors were with higher risks for congenital heart disease. Conclusion: Women of childbearing age who took cold medicine, antibiotics, salicylic acid drugs, antifungal drugs and other drugs during early pregnancy would increase the risks related to congenital heart diseases.

Authors' Reply

Authors' Reply to the Letter to the Editor by Montgomery et al (Identification of Germline Variants in Tumor Genomic Sequencing Analysis. J Mol Diagn 2017, 19:XXXX-XXXX).

Clinical Impact of Genomic Information in Pediatric Leukemia

Pediatric leukemia remains a significant contributor to childhood lethality rates. However, recent development of new technologies including next-generation sequencing (NGS) has increased our understanding of the biological and genetic underpinnings of leukemia, resulting in novel diagnostic and treatment paradigms. The most prevalent pediatric leukemias include B-cell acute lymphoblastic leukemia (B-ALL) and acute myeloid leukemia (AML). These leukemias are highly heterogeneous, both clinically and genetically. There are multiple genetic subgroups defined by the World Health Organization, each with distinct clinical management. Clinical laboratories have started adopting genomic testing strategies to include high-throughput sequencing assays which, together with conventional cytogenetic techniques, enable optimal patient care. This review summarizes genetic and genomic techniques used in clinical laboratories to support management of pediatric leukemia, highlighting technical, biological, and clinical advances. We illustrate clinical utilities of comprehensive genomic evaluation of leukemia genomes through clinical case examples, which includes the interrogations of hundreds of genes and multiple mutation mechanisms using NGS technologies. Finally, we provide a future perspective on clinical genomics and precision medicine.

Low PTEN levels and PIK3CA mutations predict resistance to neoadjuvant lapatinib and trastuzumab without chemotherapy in patients with HER2 over-expressing breast cancer

PURPOSE

Aberrant activation of the PI3K pathway has been implicated in resistance to HER2-targeted therapy, but results of clinical trials are confounded by the co-administration of chemotherapy. We investigated the effect of perturbations of this pathway in breast cancers from patients treated with neoadjuvant anti-HER2-targeted therapy without chemotherapy.

PATIENTS AND METHODS

Baseline tumor samples from patients with HER2-positive breast cancer enrolled in TBCRC006 (NCT00548184), a 12-week neoadjuvant clinical trial with lapatinib plus trastuzumab [plus endocrine therapy for estrogen receptor (ER)-positive tumors], were assessed for PTEN status by immunohistochemistry and PIK3CA mutations by sequencing. Results were correlated with pathologic complete response (pCR).

RESULTS

Of 64 evaluable patients, PTEN immunohistochemistry and PIK3CA mutation analysis were performed for 59 and 46 patients, respectively. PTEN status (dichotomized by H-score median) was correlated with pCR (32% in high PTEN vs. 9% in low PTEN, p = 0.04). PIK3CA mutations were identified in 14/46 tumors at baseline (30%) and did not correlate with ER or PTEN status. One patient whose tumor harbored a PIK3CA mutation achieved pCR (p = 0.14). When considered together (43 cases), 1/25 cases (4%) with a PIK3CA mutation and/or low PTEN expression levels had a pCR compared to 7/18 cases (39%) with wild-type PI3KCA and high PTEN expression levels (p = 0.006).

CONCLUSION

PI3K pathway activation is associated with resistance to lapatinib and trastuzumab in breast cancers, without chemotherapy. Further studies are warranted to investigate how to use these biomarkers to identify upfront patients who may respond to anti-HER2 alone, without chemotherapy.

[Predictive value of serial platelet function testing on outcome in patients undergoing complex percutaneous coronary intervention]

Objective: To observe the predictive value of serial platelet function testing (PFT) on outcome in patients undergoing complex percutaneous coronary intervention (PCI). Methods: Six hundred and two consecutive patients undergoing complex PCI in Anzhen hospital were enrolled during October 2011 to June 2012.Adenosine diphosphate(ADP)-induced platelet aggregation was measured by light transmission aggregometry on the first, sixth and twelfth month after PCI and the mean value was calculated.The cut-off value of high on-treatment platelet reactivity (HTPR) was defined as 40%.The primary endpoint was major adverse cardiovascular and cerebral event (MACCE). Clinical outcomes were analyzed by the Kaplan-Meier method and differences were compared using the log-rank test.Multivariate analyses by Cox proportion hazards regression were applied to identify variables independently associated with the adverse outcomes. Results: Five hundred and eighty-five patients (HTPR, n=285; non-HTPR, n=280) finished the follow-up ((28.47±7.45) months). A total of 33 cases of MACCE were observed during the follow-up, among which 29 cases(8.42%) were in HTPR group and 9 cases (3.21%) in the non-HTPR group.Kaplan-Meier analysis suggested that HTPR was associated with an increased incidence of MACCE (log-rank test, P=0.01). The Cox multivariate analysis indicated that HTPR was an independent risk factor of MACCE (HR=2.69, 95%CI 1.23-5.85, P=0.01) in patients undergoing complex PCI.Incidence of MACCE was similar between HTRP patients receiving standard dual antiplatelet therapy (DAPT) or prolonged DAPT (>12 months). Conclusion: Serial PFT could predict the long-term prognosis of patients underwent complex PCI.

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists

Widespread clinical laboratory implementation of next-generation sequencing-based cancer testing has highlighted the importance and potential benefits of standardizing the interpretation and reporting of molecular results among laboratories. A multidisciplinary working group tasked to assess the current status of next-generation sequencing-based cancer testing and establish standardized consensus classification, annotation, interpretation, and reporting conventions for somatic sequence variants was convened by the Association for Molecular Pathology with liaison representation from the American College of Medical Genetics and Genomics, American Society of Clinical Oncology, and College of American Pathologists. On the basis of the results of professional surveys, literature review, and the Working Group's subject matter expert consensus, a four-tiered system to categorize somatic sequence variations based on their clinical significances is proposed: tier I, variants with strong clinical significance; tier II, variants with potential clinical significance; tier III, variants of unknown clinical significance; and tier IV, variants deemed benign or likely benign. Cancer genomics is a rapidly evolving field; therefore, the clinical significance of any variant in therapy, diagnosis, or prognosis should be reevaluated on an ongoing basis. Reporting of genomic variants should follow standard nomenclature, with testing method and limitations clearly described. Clinical recommendations should be concise and correlate with histological and clinical findings.

Effects of dirty housing and a Typhimurium DT104 challenge on pig growth performance, diet utilization efficiency, and gas emissions from stored manure

The objectives of this study were to elucidate the effects of a dirty environment and a challenge plus associated environmental contamination on pig growth performance, diet utilization efficiency, and gas emissions (CO, NH, CH, NO, and HS) from stored manure. Twenty-four weaned barrows, aged 31 d at initiation of the trial, were randomly allotted to 3 different treatments in a completely randomized design. Treatments were: pigs housed in cages with manure removed and cages washed daily (Clean); pigs housed in cages sprayed daily with manure slurry mixtures (Dirty); or pigs challenged with Typhimurium DT104 and housed in cages that were not washed, but manure was removed daily ( challenge). Rectal temperature, body weight, daily feed intake, manure output, manure composition, and gas emissions from stored manure were measured throughout the 24-d animal phase. The Dirty and challenge treatments were statistically compared to the Clean treatment to evaluate individual effects. Dirty housing tended to decrease ADG from d 1 to 24 ( = 0.06) but there were no other effects on pig performance compared with the Clean treatment. In contrast, a challenge was associated with a marked reduction in each of the measured indicators of pig performance. challenge increased the carbon to nitrogen ratio, ether extract, and lignin concentrations in excreted manure ( = 0.02, 0.01, 0.003, respectively), and increased manure and head space temperatures in manure tanks ( < 0.0001). Gas emissions from stored manure of pigs on the Dirty or treatments were increased for each of the measured gases as compared to the Clean treatment ( < 0.01) when expressed per unit of BW gain. When gas emissions from manure of pigs housed in the Dirty treatment were expressed per unit of manure volatile solids (VS), they were increased for NH, CH, and HS ( < 0.02). challenge was associated with increased emissions of CO, and NO and decreased emissions of HS per kilogram manure VS compared to the Clean treatment ( = 0.06, 0.03, 0.04, respectively). Collectively, these results indicated that a challenge and associated housing contamination caused depressed growth rate and increased manure gas emissions, while exposure to a Dirty environment slightly reduced growth performance and clearly increased manure gas emissions per unit of BW gain as compared to Clean control.

[Utility of texture analysis of magnetic resonance imaging in differential diagnosis of common pediatric cerebellar tumors in children]

OBJECTIVE

To analyze magnetic resonance images of the posterior cranial fossa tumors, and evaluate the texture characteristics of three kinds of children's posterior cranial fossa tumors by support vector machine (SVM).

METHODS

From May 2008 to August 2015, a total of 76 patients with children's posterior cranial fossa tumors in First Affiliated Hospital of Zhengzhou University were retrospectively analyzed, texture analysis was performed on the three types of tumors.

RESULTS

The 5 texture parameters extracted from the gray level co-occurrence matrix had at least 3 parameters which had statistically significant difference between the two different classes of data sets (P<0.05). For all kinds of data sets, the variance parameters of gray value of ROI region had statistically significant differences.The accuracy rate of SVM test in the remarkable difference of the ependymomas and medulloblastomas, the ependymomas and astrocytomas and the medulloblastomas and astrocytomas was 86.15%±4.16%, 73.63%±5.82% and 74.32%±5.85%, respectively.

CONCLUSION

The analysis of texture features can provide more quantitative information which could provide a new thought and method for the differential diagnosis of tumors in the posterior cranial fossa.

Effects of Epinephrine on Inflammation-Related Gene Expressions in Cultured Rat Cardiomyocytes

Epinephrine, a non-specific adrenergic agonist, is one of the most commonly used inotropes perioperatively. Recent studies have shown that inflammatory response in cardiac surgery could result in hypoperfusion, dysrhythmias, myocardial ischemia, and other pathophysiological alterations in the postoperative period. These alterations might be contributing to the adverse clinical outcome. Although epinephrine has been shown to have effects on the immune system, how epinephrine affects inflammatory response is unclear. We hypothesized that epinephrine exposure may alter the inflammatory response which may potentially contribute to the adverse clinical outcomes. We used cultured rat cardiomyocytes (H9C2) with epinephrine exposure in this study. The expression of mRNA for inflammation-related genes was quantitated for the comparison of experimental group (with epinephrine) and control group (without epinephrine). The results demonstrated significant changes of inflammation-related gene expressions in cardiomyocytes after epinephrine administration. The clinical implications of the gene expression changes in cardiomyocytes are unclear.

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.

Divergence and polymorphism analysis of IGF1Ra and IGF1Rb from orange-spotted grouper, Epinephelus coioides (Hamilton)

Orange-spotted grouper (Epinephelus coioides) is one of the most important marine fish and has a high market value. The insulin-like growth factor type 1 receptor (IGF1R) is a component of the insulin-like growth factor signaling system, and demonstrates important roles during growth. Based on information from livestock, we used IGF1R as a candidate gene to survey single nucleotide polymorphisms. In the present study, the sequences of IGF1Ra and IGF1Rb from orange-spotted grouper were obtained from the genome sequences and their clustering in clades a and b, respectively, was confirmed by phylogenetic analysis. Fourteen critical amino acids underlying functional divergence were detected between the two clades, revealing the molecular basis of their functional differences. Nearly one-fourth (22 kbp) of the genomic sequence of IGF1Ra was sequenced in a mass cross population, and nucleotide diversity and linkage disequilibrium levels were investigated. Nucleotide diversity was 0.00328 for π and 0.00344 for θ_w. The half decay of the squared allele-frequency correlation was 10,835 base pairs. Comparatively, the relatively high level of linkage and the significant deviation from neutrality-based codons in IGR1R showed that this gene was under selection. A site (KR269824.1:g. 63762C>T), located in the sixth intron, was significantly associated with eyeball diameter (P = 1.39 x 10^-4, Q-value: 2.33 x 10^-2), which accounted for 11.1% of phenotypic variance. These results highlight the important function of IGF1R in orange-spotted grouper and may be beneficial in the breeding of this species.

A two-step method for identification of the Chinese glutinous rice Suyunuo, based on ISSR-SCAR and allele-specific markers

Suyunuo is a valuable glutinous rice variety cultivated mainly in the Lake Taihu area of China. Historically, Suyunuo was presented to emperors as a tribute, and, still today, enjoys a great reputation in China. This study aimed to develop a unique, specific molecular marker for the identification of Suyunuo rice. Polymerase chain reaction (PCR) amplification of inter-simple sequence repeat (ISSR) molecular markers was performed on Suyunuo and 11 other glutinous rice varieties that are mainly cultivated in the Yangtze River Delta region. A Suyunuo-specific band was detected in the PCR products generated from primer ISSR-807. A sequence characterized amplified region (SCAR) primer pair targeting a Suyunuo-specific band was subsequently designed. The SCAR primers amplified a target band in all individuals of Suyunuo and in four glutinous indica varieties, whereas no bands were found in the seven glutinous japonica varieties. Subsequently, sequences amplified by the SCAR primer pair were analyzed to facilitate the design of Suyunuo allele-specific primers. The allele-specific primer pair produced target bands in all individuals of Suyunuo rice but no bands in individuals of any of the other 11 rice varieties. This study provides a theoretical guideline for rice germplasm identification and innovation of other valuable rice landraces.

Design of Hydrogen Storage Alloys/Nanoporous Metals Hybrid Electrodes for Nickel-Metal Hydride Batteries

Nickel metal hydride (Ni-MH) batteries have demonstrated key technology advantages for applications in new-energy vehicles, which play an important role in reducing greenhouse gas emissions and the world's dependence on fossil fuels. However, the poor high-rate dischargeability of the negative electrode materials-hydrogen storage alloys (HSAs) limits applications of Ni-MH batteries in high-power fields due to large polarization. Here we design a hybrid electrode by integrating HSAs with a current collector of three-dimensional bicontinuous nanoporous Ni. The electrode shows enhanced high-rate dischargeability with the capacity retention rate reaching 44.6% at a discharge current density of 3000 mA g(-1), which is 2.4 times that of bare HSAs (18.8%). Such a unique hybrid architecture not only enhances charge transfer between nanoporous Ni and HSAs, but also facilitates rapid diffusion of hydrogen atoms in HSAs. The developed HSAs/nanoporous metals hybrid structures exhibit great potential to be candidates as electrodes in high-performance Ni-MH batteries towards applications in new-energy vehicles.

Analysis of genetic diversity of Brassica rapa var. chinensis using ISSR markers and development of SCAR marker specific for Fragrant Bok Choy, a product of geographic indication

Non-heading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] is a popular vegetable and is also used as a medicinal plant in traditional Chinese medicine. Fragrant Bok Choy is a unique accession of non-heading Chinese cabbage and a product of geographic indication certified by the Ministry of Agriculture of China, which is noted for its rich aromatic flavor. However, transitional and overlapping morphological traits can make it difficult to distinguish this accession from other non-heading Chinese cabbages. This study aimed to develop a molecular method for efficient identification of Fragrant Bok Choy. Genetic diversity analysis, based on inter-simple sequence repeat molecular markers, was conducted for 11 non-heading Chinese cabbage accessions grown in the Yangtze River Delta region. Genetic similarity coefficients between the 11 accessions ranged from 0.5455 to 0.8961, and the genetic distance ranged from 0.0755 to 0.4475. Cluster analysis divided the 11 accessions into two major groups. The primer ISSR-840 amplified a fragment specific for Fragrant Bok Choy. A pair of specific sequence-characterized amplified region (SCAR) primers based on this fragment amplified a target band in Fragrant Bok Choy individuals, but no band was detected in individuals of other accessions. In conclusion, this study has developed an efficient strategy for authentication of Fragrant Bok Choy. The SCAR marker described here will facilitate the conservation and utilization of this unique non-heading Chinese cabbage germplasm resource.

Optimization of polarizer azimuth in improving signal-to-noise ratio in Kerr microscopy

The magneto optical Kerr effect (MOKE) is a widely used technique in magnetic domain imaging for its high surface sensitivity and external magnetic compatibility. Optimization of Kerr microscopy will improve the detecting sensitivity and provide high-quality domain images. In this work, we provide a method to optimize the polarizer azimuth in improving the signal-to-noise ratio (S/N) in longitudinal Kerr microscopy with the generalized magneto optical ellipsometry. Detailed analysis of the MOKE signal and the noise components are provided to study the optimum polarizer and analyzer azimuth combinations. Results show that, for a fixed polarizer angle 1°, the laser intensity noise and the shot noise, which vary with the input laser power, have a similar amplitude and decline with the analyzer azimuth increasing. When the analyzer is set at the extinction place, the Johnson noise plays a dominate role in the total noise. Then, the S/N values are calculated to find the optimum polarizer and analyzer azimuth. Results show that the optimum polarizer and analyzer azimuth combination for Permalloy is (18.35°, 68.35°) under an incident angle of 45°. After that, the S/N of 200 nm Permalloy at different analyzer angles with the polarizer azimuth set at 18.35° is measured to verify the validity of the simulation results. At last, the S/N at different incident angles is calculated. Results show that the optimum incident angle of 200 nm Permalloy film to improve the S/N is 70.35° under the polarizer and analyzer angles set at the optimal combinations (18.35°, 68.35°).

Transcriptomic analysis of Camellia ptilophylla and identification of genes associated with flavonoid and caffeine biosynthesis

Camellia ptilophylla, or cocoa tea, is naturally decaffeinated and its predominant catechins and purine alkaloids are trans-catechins and theobromine Regular tea [Camellia sinensis (L.) O. Ktze.] is evolutionarily close to cocoa tea and produces cis-catechins and caffeine. Here, the transcriptome of C. ptilophylla was sequenced using the 101-bp paired-end technique. The quality of the raw data was assessed to yield 70,227,953 cleaned reads totaling 7.09 Gbp, which were assembled de novo into 56,695 unique transcripts and then clustered into 44,749 unigenes. In catechin biosynthesis, leucoanthocyanidin reductase (LAR) catalyzes the transition of leucoanthocyanidin to trans-catechins, while anthocyanidin synthase (ANS) and anthocyanidin reductase (ANR) catalyze cis-catechin production. Our data demonstrate that two LAR genes (CpLAR1 and CpLAR2) by C. ptilophylla may be advantageous due to the combined effects of this quantitative trait, permitting increased leucoanthocyanidin consumption for the synthesis of trans-catechins. In contrast, the only ANS gene observed in C. sinensis (CsANS) shared high identity (99.2%) to one homolog from C. ptilophylla (CpANS1), but lower identity (~80%) to another (CpANS2). We hypothesized that the diverged CpANS2 might have lost its ability to synthesize cis-catechins. C. ptilophylla and C. sinensis each contain two copies of ANR, which share high identity and may share the same function. Transcriptomic sequencing captured two N-methyl nucleosidase genes named NMT1 and NMT2. NMT2 was highly identical to three orthologous genes TCS2, PCS2, and ICS2, which did not undergo methylation in vitro; in contrast, NMT1 was less identical to TCS, PCS and ICS, indicating that NMT1 may undergo neofunctionalization.

Cloning and prokaryotic expression of the porcine lipasin gene

Lipasin has recently been demonstrated to be involved in lipid metabolism. In this study, two specific primers were used to amplify the lipasin open reading frame from porcine liver tissue. The polymerase chain reaction product was cloned to a pGEM®-T Easy Vector, digested by SalI and NotI, and sequenced. The lipasin fragment was then cloned to a pET21(b) vector and digested by the same restriction enzyme. The recombinant plasmid was transferred to Escherichia coli (BL21), and the lipasin protein was induced with isopropyl-β-D-thiogalactopyranoside. The protein obtained was identified by sodium dodecyl sulfate polyacrylamide gel electrophoresis and western blotting. A pET-lipasin prokaryotic recombinant expression vector was successfully constructed, and a 25.2-kDa protein was obtained. This study provides a basis for further research on the biological function of porcine lipasin.