• RNA sequencing
• next-generation sequencing
• personalized treatment
• whole-exome sequencing
• whole-genome sequencing

• EGFR
• RNAseq analysis
• fibrous hamartoma of infancy
• kinase aberrations
• mesenchymal tumors
• mesenchymal tumors with kinase fusions
• methylation profiling
• mutations

• Humans
• Male
• Female
• ErbB Receptors/genetics
• Child
• Child, Preschool
• Adolescent
• Infant
• Retrospective Studies
• Mutation
• Soft Tissue Neoplasms/genetics
• Soft Tissue Neoplasms/pathology
• Soft Tissue Neoplasms/enzymology
• Biomarkers, Tumor/genetics
• Biomarkers, Tumor/analysis
• DNA Methylation
• Immunohistochemistry

• tumour biomarkers
• non-small-cell lung cancer

• Carcinoma, Non-Small-Cell Lung/genetics
• Humans
• High-Throughput Nucleotide Sequencing/methods
• High-Throughput Nucleotide Sequencing/standards
• Lung Neoplasms/genetics
• Circulating Tumor DNA/genetics
• Circulating Tumor DNA/blood

• FFPE
• FGFR3::TACC3 fusion
• RT-PCR
• glioblastoma

• CP: Cancer
• patient-derived organoids
• radioresistance
• rectal cancer
• single-cell sequencing
• tumor evolution

• Humans
• Rectal Neoplasms/genetics
• Rectal Neoplasms/radiotherapy
• Cell Line
• Chromosomal Instability
• Karyotype
• Organoids

• cancer microenvironment
• colorectal cancer
• imaging the immune system

• Humans
• CD8-Positive T-Lymphocytes
• DNA Mismatch Repair
• Prognosis
• Colonic Neoplasms
• Colorectal Neoplasms/pathology
• Microsatellite Instability
• Rectal Neoplasms
• Tumor Microenvironment

• UU-10660 KWF Kankerbestrijding (Dutch Cancer Society)
• Dutch Scientific Organization (NWO Gravitation) Grant reference number: 024.001.028

• Formalin-fixed paraffin - embedded
• Metagenomic next-generation sequencing
• Molecular pathology
• Mycobacterium granuloma
• Xpert MTB/RIF

• Humans
• Paraffin Embedding
• Mycobacterium/genetics
• Tuberculosis/microbiology
• Formaldehyde
• High-Throughput Nucleotide Sequencing
• Granuloma/diagnosis
• Mycobacterium tuberculosis/genetics
• Retrospective Studies
• Metagenomics

• Craniosynostosis
• Epilepsy
• Hydrocephalus
• NGS
• Next-Generation Sequencing
• Pediatric Neurosurgery
• WES
• Whole-exome Sequencing

• Microdissection
• Nucleic acid isolation
• Tissue dissection

• Humans
• Carcinoma, Non-Small-Cell Lung
• Prognosis
• Lung Neoplasms
• Dissection/methods
• Microdissection/methods
• Tissue Fixation/methods
• Paraffin Embedding/methods

• P50 CA062924 NCI NIH HHS
• R01 GM130564 NIGMS NIH HHS
• R01 HL137811 NHLBI NIH HHS
• T32 GM007814 NIGMS NIH HHS

Development of next-generation sequencing (NGS) has provided useful genetic information to redefine diagnostic, prognostic, and therapeutic strategies for the management of acute leukemia (AL). However, the application in the clinical setting is still challenging. Our aim was to validate the AmpliSeq™ for Illumina® Childhood Cancer Panel, a pediatric pan-cancer targeted NGS panel that includes the most common genes associated with childhood cancer, and assess its utility in the daily routine of AL diagnostics. In terms of sequencing metrics, the assay reached all the expected values. We obtained a mean read depth greater than 1000×. The panel demonstrated a high sensitivity for DNA (98.5% for variants with 5% variant allele frequency (VAF)) and RNA (94.4%), 100% of specificity and reproducibility for DNA and 89% of reproducibility for RNA. Regarding clinical utility, 49% of mutations and 97% of the fusions identified were demonstrated to have clinical impact. Forty-one percent of mutations refined diagnosis, while 49% of them were considered targetable. Regarding RNA, fusion genes were more clinically impactful in terms of refining diagnostic (97%). Overall, the panel found clinically relevant results in the 43% of patients tested in this cohort. To sum up, we validated a reliable and reproducible method to refine pediatric AL diagnosis, prognosis, and treatment, and demonstrated the feasibility of incorporating a targeted NGS panel into pediatric hematology practice.

• FFPE
• Liquid biopsy
• Molecular pathology
• Next-generation sequencing
• Preanalytical variable
• Variant calling
• ctDNA

• Gene Library
• High-Throughput Nucleotide Sequencing/methods
• Humans
• Neoplasms/diagnosis
• Neoplasms/genetics
• Precision Medicine
• Quality Control

• Epidermal growth factor receptor
• Lung adenocarcinoma
• Lung neoplasms
• Next-generation sequencing
• Non-small cell lung cancer
• Polymerase chain reaction

Genomic testing gives guidance to the treatment options in lung adenocarcinoma patients, but some patients are unable to obtain tissue samples due to lesion location or intolerance. Cell-free circulating tumor DNA (ctDNA) tested in plasma or pleural effusion is an advanced access to solve the problem. Our study descriptively identified the genetic variations of advanced Chinese lung adenocarcinoma patients and analyzed the overall survival of patients with EGFR mutations.

A total of 152 patients' plasma samples were included, and gene mutations were detected by NGS using an Illumina Miseq tabletop sequencer.

Frequencies of altered were EGFR 46.05%, ALK 7.24%, KRAS 6.58%, PIK3CA 6.58%, PTEN 2.63%, HER2 1.97%, MET 1.97%, BRAF 1.32%, NF1 1.32%, and ROS1 0.66%. We identified 48 cases with double or triple driver gene mutations. Multiple mutations were more frequently observed in EGFR and PIK3CA genes. Patients harboring coexistent mutations with an EGFR mutation tended to have a shorter overall survival than those with exclusively EGFR mutations.

EGFR, ALK, and KRAS were common driver gene in Chinese patients with stage IV lung adenocarcinoma. Multiple mutations were detected in the ctDNA samples and involve more EGFR and PIK3CA mutations. The existence of coexisting gene mutations may have adverse effects on the prognosis of patients with EGFR mutation. The unknown mutations discovered by NGS may provide new targets for gene targeting therapy, and ctDNA test by NGS is an effective method for making appropriate treatment choices.

• Immunotherapy
• Microsatellite instability
• Molecular profile
• Next Generation Sequencing
• PD-L1
• Targeted treatment
• Tumor mutation burden

• Humans
• Biomarkers, Tumor/genetics
• Neoplasms/genetics
• Neoplasms/therapy
• Male
• Female
• High-Throughput Nucleotide Sequencing
• Middle Aged
• Aged
• Microsatellite Instability
• Immunotherapy
• Adult
• Mutation
• Aged, 80 and over
• B7-H1 Antigen/genetics
• B7-H1 Antigen/metabolism

Nodular fasciitis is usually a benign lesion genetically characterized by ubiquitin-specific protease 6 (USP6) rearrangements. We present a case of a 10-year-old boy with a 1.5-week history of a painless mass on the right chest wall, which was excised. A histomorphologically malignant tumor with pronounced pleomorphism, atypical mitotic figures, and a myoid immunophenotype was observed. The methylation profile was consistent with nodular fasciitis and fluorescence in situ hybridization confirmed USP6 rearrangement. Using Archer Fusion Plex (Sarcoma Panel) and RNA sequencing, a collagen, type VI, alpha 2 (COL6A2)–USP6 gene fusion was subsequently identified. Furthermore, DNA clustering analysis also showed a match with nodular fasciitis. During the follow-up of 22 months, no recurrence or metastasis occurred. In conclusion, we describe a clinically benign, histomorphologically malignant mesenchymal neoplasm with a myoid immunophenotype, and a genetic and epigenetic profile consistent with nodular fasciitis. In such cases, molecular analysis is a useful adjunct to avoid unnecessary overtreatment.

• COL6A2–USP6
• DNA-cluster analysis
• clustering
• fusion gene
• methylation profiling
• nodular fasciitis
• pleomorphic sarcoma

Glioblastoma (GBM) is the most malignant primary brain tumor, for which improving patient outcome is limited by a substantial amount of tumor heterogeneity. Magnetic resonance imaging (MRI) in combination with machine learning offers the possibility to collect qualitative and quantitative imaging features which can be used to predict patient prognosis and relevant tumor markers which can aid in selecting the right treatment. This study showed that combining these MRI features with clinical features has the highest prognostic value for GBM patients; this model performed similarly in an independent GBM cohort, showing its reproducibility. The prediction of tumor markers showed promising results in the training set but not could be validated in the independent dataset. This study shows the potential of using MRI to predict prognosis and tumor markers, but further optimization and prospective studies are warranted.

Glioblastoma (GBM) is the most malignant primary brain tumor for which no curative treatment options exist. Non-invasive qualitative (Visually Accessible Rembrandt Images (VASARI)) and quantitative (radiomics) imaging features to predict prognosis and clinically relevant markers for GBM patients are needed to guide clinicians. A retrospective analysis of GBM patients in two neuro-oncology centers was conducted. The multimodal Cox-regression model to predict overall survival (OS) was developed using clinical features with VASARI and radiomics features in isocitrate dehydrogenase (IDH)-wild type GBM. Predictive models for IDH-mutation, 06-methylguanine-DNA-methyltransferase (MGMT)-methylation and epidermal growth factor receptor (EGFR) amplification using imaging features were developed using machine learning. The performance of the prognostic model improved upon addition of clinical, VASARI and radiomics features, for which the combined model performed best. This could be reproduced after external validation (C-index 0.711 95% CI 0.64–0.78) and used to stratify Kaplan–Meijer curves in two survival groups (p-value < 0.001). The predictive models performed significantly in the external validation for EGFR amplification (area-under-the-curve (AUC) 0.707, 95% CI 0.582–8.25) and MGMT-methylation (AUC 0.667, 95% CI 0.522–0.82) but not for IDH-mutation (AUC 0.695, 95% CI 0.436–0.927). The integrated clinical and imaging prognostic model was shown to be robust and of potential clinical relevance. The prediction of molecular markers showed promising results in the training set but could not be validated after external validation in a clinically relevant manner. Overall, these results show the potential of combining clinical features with imaging features for prognostic and predictive models in GBM, but further optimization and larger prospective studies are warranted.

• MRI
• glioblastoma
• machine learning
• prediction
• prognosis
• radiomics
• survival

• Biomarker
• Ethics
• Health economics
• Liquid biopsies
• Molecular and digital pathology
• Molecular imaging
• Omics technologies
• Patient management
• Pharmacology
• Sample quality
• Theranostics
• Treatment

• clinical practice
• genetic testing
• neurogenesis
• next generation sequencing
• sequencing approaches
• variant interpretation

• DNA integrity
• formalin-fixed paraffin-embedded tumor tissue
• next-generation sequencing
• quality control

• DNA, Neoplasm/analysis
• High-Throughput Nucleotide Sequencing/methods
• Humans
• Japan
• Paraffin Embedding
• Pathology, Molecular/methods
• Tissue Fixation

• H26-Policy for Cancer General-005 Health, Labor, and Welfare Sciences Research Grants
• 28-A-5 and 31-A-2 The National Cancer Research and Development Fund
• JP18ck0106233h0003 Japan Agency for Medical Research and Development
• Japan Agency for Medical Research and Development

The development of Next-Generation Sequencing (NGS) has provided useful diagnostic, prognostic, and therapeutic strategies for individualized management of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. Consequently, NGS is rapidly being established in clinical practice. However, the technology’s complexity, bioinformatics analysis, and the different available options difficult a broad consensus between different laboratories in its daily routine introduction. This collaborative study among Spanish centers was aimed to assess the feasibility, pros, and cons of our customized panel and other commercial alternatives of NGS-targeted approaches. The custom panel was tested in three different sequencing centers. We used the same samples to assess other commercial panels (Oncomine^TM Childhood Cancer Research Assay; Archer^®FusionPlex^® ALL, and Human Comprehensive Cancer Panel GeneRead Panel v2^®). Overall, the panels showed a good performance in different centers and platforms, but each NGS approach presented some issues, as well as pros and cons. Moreover, a previous consensus on the analysis and reporting following international guidelines would be preferable to improve the concordance in results among centers. Our study shows the challenges posed by NGS methodology and the need to consider several aspects of the chosen NGS-targeted approach and reach a consensus before implementing it in daily practice.

• NGS-targeted panel
• childhood acute lymphoblastic leukemia
• next-generation sequencing

• Parkinson's disease
• SNCA
• molecular barcodes
• somatic mutation
• synuclein
• synucleinopathies
• targeted sequencing

Molecular diagnostics can be decisive in the differential diagnosis between a somatic metastasis of type II testicular germ cell tumor (TGCT) or a second primary carcinoma. This is in line with recent recommendations from the International Society of Urological Pathology, based on an international survey which showed that molecular testing is currently only performed by a minority of urological pathologists.

This case report illustrates the necessity of molecular testing in two patients with a history of type II TGCT and a metastatic (retro) peritoneal carcinoma years later. The genetic hallmark of type II TGCT, chromosome 12p gain, was studied by fluorescence in situ hybridization and whole genome methylation profiling in case 1, and by single nucleotide polymorphism (SNP)-array in case 2. Next generation sequencing (NGS) was used to further explore clonality between the primary TGCT and peritoneal metastasis in case 2. In case 1, chromosome 12p gain was found in the primary type II TGCT and in the acinar cell carcinoma of the metastatic malignancy. In case 2, SNP array showed 12p gain in the epithelial component of the primary teratomatous TGCT but not in the peritoneal adenocarcinoma. Furthermore, NGS showed no mutations in the primary teratomatous TGCT but a KRAS and GNAS mutation in the peritoneal adenocarcinoma, suggestive of an appendicular origin.

Without the molecular data, both cases would have been regarded as a metastatic TGCT with development of somatic-type malignancy, which appeared a wrong diagnosis for case 2. These cases demonstrate the importance of molecular methods as an adjunct in today’s pathology practice.

• Case report
• Gain 12p
• Metastasis
• Molecular diagnostics
• Testicular germ cell tumor

• EURACAN
• ITMIG
• TCGA
• biobank
• microRNA
• thymic carcinoma
• thymic epithelial tumors
• thymoma

• cancer
• cancer epidemiology
• cancer genetics
• cancer genomics
• head and neck cancer
• oral cancer

• Adult
• Aged
• Carcinoma, Squamous Cell/genetics
• Carcinoma, Squamous Cell/virology
• Cohort Studies
• Disease-Free Survival
• Female
• High-Throughput Nucleotide Sequencing/methods
• Humans
• Male
• Middle Aged
• Mutation/genetics
• Neoplasm Recurrence, Local/genetics
• Neoplasm Recurrence, Local/virology
• Oropharyngeal Neoplasms/genetics
• Oropharyngeal Neoplasms/virology
• Papillomaviridae/pathogenicity
• Papillomavirus Infections/virology
• Nicotiana/adverse effects

• cancer
• molecular pathology
• next-generation sequencing
• personalized medicine
• precision medicine
• precision oncology

• Maturity-onset diabetes of the young
• Sanger sequencing
• molecular diagnostics
• monogenic diabetes mellitus
• multiplex
• neonatal diabetes
• next-generation sequencing

How and when tumoral clones start spreading to surrounding and distant tissues is currently unclear. Here we leveraged a model-based evolutionary framework to investigate the demographic and biogeographic history of a colorectal cancer. Our analyses strongly support an early monoclonal metastatic colonization, followed by a rapid population expansion at both primary and secondary sites. Moreover, we infer a hematogenous metastatic spread under positive selection, plus the return of some tumoral cells from the liver back to the colon lymph nodes. This study illustrates how sophisticated techniques typical of organismal evolution can provide a detailed, quantitative picture of the complex tumoral dynamics over time and space.

The clonal origins of metastases and the timing of dissemination remains an open question for most cancer types. Using primary and metastatic samples taken from one colorectal cancer patient, Alves et al. use Bayesian phylogenetics to reconstruct the history of metastasis.

• Colon Cancer
• Complication
• Metastasis
• Recurrence

Next Generation Sequencing (NGS) is a promising tool for the improvement of tumor molecular profiling in view of the identification of a personalized treatment in oncologic patients. To verify the potentiality of a targeted NGS (Ion AmpliSeq™ Cancer Hotspot Panel v2), selected melanoma samples (n = 21) were retrospectively analyzed on S5 platform in order to compare NGS performance with the conventional techniques adopted in our routine clinical setting (Sequenom MassARRAY system, Sanger sequencing, allele-specific real-time PCR). The capability in the identification of rare and low-frequency mutations in the main genes involved in melanoma (BRAF and NRAS genes) was verified and integrated with the results deriving from other oncogenes and tumor suppressor genes. The analytical evaluation was carried out by the analysis of DNA derived from control cell lines and FFPE (Formalin-Fixed, Paraffin-Embedded) samples to verify that the achieved resolution of uncommon mutations and low-frequency variants was suitable to meet the technical and clinical requests. Our results demonstrate that the amplicon-based NGS approach can reach the sensitivity proper of the allele-specific assays together with the high specificity of a sequencing method. An overall concordance among the tested methods was observed in the identification of classical and uncommon mutations. The assessment of the quality parameters and the comparison with the orthogonal methods suggest that the NGS method could be implemented in the clinical setting for melanoma molecular characterization.

• BRAF V-raf murine sarcoma viral oncogene homolog B
• melanoma
• next generation sequencing
• sequenom MassARRAY system
• somatic mutation

The introduction of fast and robust whole slide scanners has facilitated the implementation of ‘digital pathology’ with various uses, the final challenge being full digital diagnostics. In this article, we describe the implementation process of a fully digital workflow for primary diagnostics in 2015 at the University Medical Centre in Utrecht, The Netherlands, as one of the first laboratories going fully digital with a future‐proof complete digital archive. Furthermore, we evaluated the experience of the first 2 years of working with the system by pathologists and residents. The system was successfully implemented in 6 months, including a European tender procedure. Most pathologists and residents had high confidence in working fully digitally, the expertise areas lagging behind being paediatrics, haematopathology, and neuropathology. Reported limitations concerned recognition of microorganisms and mitoses. Neither the age of respondents nor the number of years of pathology experience was correlated with the confidence level regarding digital diagnostics. The ergonomics of digital diagnostics were better than those of traditional microscopy. In this article, we describe our experiences in implementing our fully digital primary diagnostics workflow, describing in depth the implementation steps undertaken, the interlocking components that are required for a fully functional digital pathology system (laboratory management, hospital information systems, data storage, and whole slide scanners), and the changes required in workflow and slide production.

• diagnostics
• digital pathology
• digital primary diagnostics
• implementation
• laboratory management

• UNE-EN ISO 15189 accreditation
• metastatic colorectal cancer
• molecular diagnostics
• next generation sequencing
• non-small cell lung cancer

• RTC-2015-3625-1 Ministerio de Economía, Industria y Competitividad, Programa Estatal de I+D+i Orientada a los Retos de la Sociedad, Convocatoria Retos-Colaboración 2015
• IISLaFe 2017/0070 Roche Diagnostics
• ACIF/2018/258 Consellería de Educación, Investigación, Cultura y Deporte de la Comunidad Valenciana

• DNA integrity number
• Formalin-fixed paraffin-embedded
• Next-generation sequencing
• Preanalytical
• Quality metrics
• Tissue harvesting

Acinar cell carcinoma (ACC) is a rare pancreatic neoplasm with dismal prognosis. Insights into the molecular basis of ACC can pave the way for the application of more effective, personalized therapies and detection of patients with hereditary predisposition.

Molecular analysis revealed a germline BRCA2 (and CHEK2) mutation in a patient with a rare pancreatic ACC with extensive intraductal growth. Somatic loss of the wild-type BRCA2 allele in the tumor indicated the causal relationship of ACC with the germline defect. A thorough literature review identified another nine ACCs associated with germline BRCA2 mutation and two ACCs associated with germline BRCA1 mutation, resulting in a prevalence of BRCA1/2 germline mutations in almost 7% of ACCs. Moreover, somatic BRCA1/2 alterations are reported in 16% of sporadic ACCs. Overall, about one fifth (22%) of all pancreatic ACCs exhibit BRCA1/2 deficiency.

This study underscores the important role of BRCA1/2 mutations in pancreatic ACC. All ACC patients should undergo genetic testing for BRCA1/2 mutations to identify carriers of pathogenic variants. This will allow to select patients that can benefit from targeted therapies directed against BRCA1/2-deficient tumors and is also crucial as a referral to genetic screening for the relatives of affected individuals carrying germline BRCA1/2 alterations.

Abbreviations: ACC: acinar cell carcinoma; HBOC: Hereditary Breast and Ovarian Cancer; LOH: loss of heterozygosity; PARP: poly (ADP-ribose) polymerase; PDAC: pancreatic ductal adenocarcinoma; PP: pancreatic panniculitis; SD: standard deviation; WES: whole-exome sequencing.

• Acinar cell carcinoma of the pancreas
• germline mutation
• somatic mutation