Correction: Personalized Precision Medicine for Health Care Professionals: Development of a Competency Framework.

[This corrects the article DOI: 10.2196/43656.].

Personalized Precision Medicine for Health Care Professionals: Development of a Competency Framework.

BACKGROUND: Personalized precision medicine represents a paradigm shift and a new reality for the health care system in Spain, with training being fundamental for its full implementation and application in clinical practice. In this sense, health care professionals face educational challenges related to the acquisition of competencies to perform their professional practice optimally and efficiently in this new environment. The definition of competencies for health care professionals provides a clear guide on the level of knowledge, skills, and attitudes required to adequately carry out their professional practice. In this context, this acquisition of competencies by health care professionals can be defined as a dynamic and longitudinal process by which they use knowledge, skills, attitudes, and good judgment associated with their profession to develop it effectively in all situations corresponding to their field of practice. OBJECTIVE: This report aims to define a proposal of essential knowledge domains and common competencies for all health care professionals, which are necessary to optimally develop their professional practice within the field of personalized precision medicine as a fundamental part of the medicine of the future. METHODS: Based on a benchmark analysis and the input and expertise provided by a multidisciplinary group of experts through interviews and workshops, a new competency framework that would guarantee the optimal performance of health care professionals was defined. As a basis for the development of this report, the most relevant national and international competency frameworks and training programs were analyzed to identify aspects that are having an impact on the application of personalized precision medicine and will be considered when developing professional competencies in the future. RESULTS: This report defines a framework made up of 58 competencies structured into 5 essential domains: determinants of health, biomedical informatics, practical applications, participatory health, and bioethics, along with a cross-cutting domain that impacts the overall performance of the competencies linked to each of the above domains. Likewise, 6 professional profiles to which this proposal of a competency framework is addressed were identified according to the area where they carry out their professional activity: health care, laboratory, digital health, community health, research, and management and planning. In addition, a classification is proposed by progressive levels of training that would be advisable to acquire for each competency according to the professional profile. CONCLUSIONS: This competency framework characterizes the knowledge, skills, and attitudes required by health care professionals for the practice of personalized precision medicine. Additionally, a classification by progressive levels of training is proposed for the 6 professional profiles identified according to their professional roles.

Further definition of the proximal 19p13.3 microdeletion/microduplication syndrome and implication of PIAS4 as the major contributor.

The proximal 19p13.3 microdeletion/microduplication (prox19p13.3del/dup) syndrome is a recently described disorder with common clinical features including developmental delay, intellectual disability, speech delay, facial dysmorphic features with ear defects, anomalies of the hands and feet, umbilical hernia and hypotonia. While deletions are associated with macrocephaly, patients with duplications have microcephaly. The smallest region of overlap in multiple patients (113.5 kb) included three genes and one pseudogene, with a suggested major role of PIAS4 in determination of the phenotype and head size in these patients. Here, we refine the prox19p13.3del/dup with four additional patients: two with microdeletions, one with microduplication and one family with single-nucleotide nonsense variant in PIAS4. The patient with the PIAS4 loss of function variant displayed a phenotype quite similar to deletion patients -including the macrocephaly and many other core features of the syndrome. Patient's SNV was inherited from her mother who is similarly affected. Thus, our data indicate that PIAS4 is a major contributor to the proximal 19p13.3del/dup syndrome phenotype. In summary, we report the first patient with a pathogenic variant in PIAS4- and three additional rearrangements at the proximal 19p13.3 locus. These observations add further evidence about the molecular basis of this microdeletion/microduplication syndrome.

Recommendations for the use of microarrays in prenatal diagnosis. / Recomendaciones para el uso de microarrays en el diagnóstico prenatal.

Microarray technology, recently implemented in international prenatal diagnosis systems, has become one of the main techniques in this field in terms of detection rate and objectivity of the results. This guideline attempts to provide background information on this technology, including technical and diagnostic aspects to be considered. Specifically, this guideline defines: the different prenatal sample types to be used, as well as their characteristics (chorionic villi samples, amniotic fluid, fetal cord blood or miscarriage tissue material); variant reporting policies (including variants of uncertain significance) to be considered in informed consents and prenatal microarray reports; microarray limitations inherent to the technique and which must be taken into account when recommending microarray testing for diagnosis; a detailed clinical algorithm recommending the use of microarray testing and its introduction into routine clinical practice within the context of other genetic tests, including pregnancies in families with a genetic history or specific syndrome suspicion, first trimester increased nuchal translucency or second trimester heart malformation and ultrasound findings not related to a known or specific syndrome. This guideline has been coordinated by the Spanish Association for Prenatal Diagnosis (AEDP, «Asociación Española de Diagnóstico Prenatal¼), the Spanish Human Genetics Association (AEGH, «Asociación Española de Genética Humana¼) and the Spanish Society of Clinical Genetics and Dysmorphology (SEGCyD, «Sociedad Española de Genética Clínica y Dismorfología¼).

Chronic neutrophilic leukemia: a clinical perspective.

Chronic neutrophilic leukemia (CNL) is a rare myeloproliferative neoplasm (MPN) that includes only 150 patients described to date meeting the latest World Health Organization (WHO) criteria and the recently reported CSF3R mutations. The diagnosis is based on morphological criteria of granulocytic cells and the exclusion of genetic drivers that are known to occur in others MPNs, such as BCR-ABL1, PDGFRA/B, or FGFR1 rearrangements. However, this scenario changed with the identification of oncogenic mutations in the CSF3R gene in approximately 83% of WHO-defined and no monoclonal gammopathy-associated CNL patients. CSF3R T618I is a highly specific molecular marker for CNL that is sensitive to inhibition in vitro and in vivo by currently approved protein kinase inhibitors. In addition to CSF3R mutations, other genetic alterations have been found, notably mutations in SETBP1, which may be used as prognostic markers to guide therapeutic decisions. These findings will help to understand the pathogenesis of CNL and greatly impact the clinical management of this disease. In this review, we discuss the new genetic alterations recently found in CNL and the clinical perspectives in its diagnosis and treatment. Fortunately, since the diagnosis of CNL is not based on exclusion anymore, the molecular characterization of the CSF3R gene must be included in the WHO criteria for CNL diagnosis.

Aberrant DNA methylation profile of chronic and transformed classic Philadelphia-negative myeloproliferative neoplasms.

Most DNA methylation studies in classic Philadelphia-negative myeloproliferative neoplasms have been performed on a gene-by-gene basis. Therefore, a more comprehensive methylation profiling is needed to study the implications of this epigenetic marker in myeloproliferative neoplasms. Here, we have analyzed 71 chronic (24 polycythemia vera, 23 essential thrombocythemia and 24 primary myelofibrosis) and 13 transformed myeloproliferative neoplasms using genome-wide DNA methylation arrays. The three types of chronic Philadelphia-negative myeloproliferative neoplasms showed a similar aberrant DNA methylation pattern when compared to control samples. Differentially methylated regions were enriched in a gene network centered on the NF-κB pathway, indicating that they may be involved in the pathogenesis of these diseases. In the case of transformed myeloproliferative neoplasms, we detected an increased number of differentially methylated regions with respect to chronic myeloproliferative neoplasms. Interestingly, these genes were enriched in a list of differentially methylated regions in primary acute myeloid leukemia and in a gene network centered around the IFN pathway. Our results suggest that alterations in the DNA methylation landscape play an important role in the pathogenesis and leukemic transformation of myeloproliferative neoplasms. The therapeutic modulation of epigenetically-deregulated pathways may allow us to design targeted therapies for these patients.

Diagnóstico prenatal y array-CGH II: gestaciones de bajo riesgo / Array-CGH in prenatal diagnosis II: low-risk pregnancies

Recientemente, la tecnología conocida como array-CGH se ha establecido como una herramienta diagnóstica de primer orden para el estudio de pacientes con anomalías congénitas, retraso mental no filiado y otras enfermedades neurológicas. Sin embargo, su utilidad como técnica de primer uso en el campo prenatal está actualmente en fase de evaluación, especialmente en embarazos de bajo riesgo. En una población de 530 gestantes con embarazos de bajo riesgo se realizó, simultáneamente, cariotipo convencional y un estudio de array-CGH para el diagnóstico prenatal. Mientras que el cariotipo detectó 3 casos (0,5%) con alteraciones citogéneticas no equilibradas (una de ellas no definida), el array-CGH detectó 8 casos con este tipo de alteraciones (1,5%), identificando el cambio indefinido detectado por cariotipo. Este estudio demuestra positivamente que el array-CGH puede ser una herramienta útil en el diagnóstico prenatal en embarazos de bajo riesgo(AU)

The array-CGH technique has recently been established as a first-tier diagnostic test for studying patients with congenital anomalies, idiopathic mental retardation and other neurological disorders. However, its use in prenatal diagnosis is still being evaluated, especially in low-risk pregnancies. A study was conducted on a population of 530 low-risk pregnancy women using both conventional karyotype and array-CGH for prenatal diagnosis. Whereas conventional karyotype detected 3 foetuses (0.5%) with unbalanced cytogenetic aberrations (one of them was undefined), array-CGH detected 8 foetuses with copy number aberrations (1.5%), and positively identified the undefined cytogenetic aberration detected using karyotype. In conclusion, this study proposes array-CGH as a useful tool in prenatal diagnosis for low-risk pregnancies(AU)

Centromere-localized breaks indicate the generation of DNA damage by the mitotic spindle.

Most carcinomas present some form of chromosome instability in combination with spindle defects. Numerical instability is likely caused by spindle aberrations, but the origin of breaks and translocations remains elusive. To determine whether one mechanism can bring about both types of instability, we studied the relationship between DNA damage and spindle defects. Although lacking apparent repair defects, primary Dido mutant cells formed micronuclei containing damaged DNA. The presence of centromeres showed that micronuclei were caused by spindle defects, and cell cycle markers showed that DNA damage was generated during mitosis. Although the micronuclei themselves persisted, the DNA damage within was repaired during S and G2 phases. DNA breaks in Dido mutant cells regularly colocalized with centromeres, which were occasionally distorted. Comparable defects were found in APC mutant cell lines, an independent system for spindle defects. On the basis of these results, we propose a model for break formation in which spindle defects lead to centromere shearing.

Overexpression and activation of EGFR and VEGFR2 in medullary thyroid carcinomas is related to metastasis.

Therapeutic options for patients with metastatic medullary thyroid carcinoma (MTC) are limited due to lack of effective treatments. Thus, there is a need to thoroughly characterize the pathways of molecular pathogenesis and to identify potential targets for therapy in MTC. Since epidermal growth factor receptor (EGFR) seems to play a crucial role for RET activation, a key feature of MTCs, and several promising EGFR/vascular endothelial growth factor receptor 2 (VEGFR2)-targeted drugs have been developed, the present study was designed to investigate whether these proteins are altered in MTCs. We used a well-characterized series of 153 MTCs to evaluate EGFR activation by sequencing and FISH analysis, and to perform EGFR and VEGFR2 immunohistochemistry. EGFR tyrosine kinase domain mutations were not a feature of MTCs; however, EGFR polysomy and a strong EGFR expression were detected in 15 and 13% of the tumors respectively. Interestingly, EGFR was significantly overexpressed in metastases compared with primary tumors (35 vs 9%, P=0.002). We also studied whether specific RET mutations were associated with EGFR status, and found a decrease in EGFR polysomies (P=0.006) and a tendency towards lower EGFR expression for the most aggressive RET mutations (918, 883). Concerning VEGFR2, metastasis showed a higher expression than primary tumors (P=2.8 x 10(-8)). In this first study investigating the relationship between EGFR, RET, and VEGFR2 in a large MTC series, we found an activation of EGFR and VEGFR2 in metastasis, using both independent and matched primary/metastasis samples. This suggests that some MTC patients may benefit from existing anti-EGFR/VEFGR2 therapies, although additional preclinical and clinical evidence is needed.

Double-staining chromogenic in situ hybridization as a useful alternative to split-signal fluorescence in situ hybridization in lymphoma diagnostics.

BACKGROUND: Malignant lymphomas are classified based on morphology, immunophenotype, genetics and clinical features. The pathological diagnosis is generally considered difficult and prone to mistakes. Since non-random chromosomal translocations are specifically involved in specific entities, their detection is an important adjunct for increasing the reliability of the diagnosis. Recently, split-signal fluorescence in situ hybridization has become available as a robust method to detect chromosomal breaks in paraffin-embedded formalin-fixed tissues. A bright field approach would bring this technology within the reach of every pathology laboratory. DESIGN AND METHODS: Our study was initiated to determine the consistency between chromogenic in situ hybridization and fluorescence in situ hybridization, both using split-signal probes developed for the detection of chromosomal breaks. Five hundred and forty cases of 11 lymphoma entities and reactive, benign lymphoid tissues, collected from eight different pathology laboratories, placed on 15 fluorescence in situ hybridization pre-stained tissue microarray slides, were double stained for the chromogenic hybridization. For each core morphology and actual signal were compared to the original fluorescence hybridization results. In addition, hematoxylin background staining intensity and signal intensity of the double-staining chromogenic in situ hybridization procedure were analyzed. RESULTS: With respect to the presence or absence of chromosomal breaks, 97% concordance was found between the results of the two techniques. Hematoxylin background staining intensity and signal intensity were found to correspond. The overall morphology after double-staining chromogenic in situ hybridization had decreased compared to the initial morphology scored after split-signal fluorescence in situ hybridization staining. CONCLUSIONS: We conclude that double-staining chromogenic in situ hybridization is equally reliable as fluorescence in situ hybridization in detecting chromosomal breaks in lymphoid tissue. Although differences in morphology, hematoxylin staining and chromogenic signal intensity vary between the tumor entities none of the entities appeared more easy or difficult to score.

Epigenetic signatures associated with different levels of differentiation potential in human stem cells.

BACKGROUND: The therapeutic use of multipotent stem cells depends on their differentiation potential, which has been shown to be variable for different populations. These differences are likely to be the result of key changes in their epigenetic profiles. METHODOLOGY/PRINCIPAL FINDINGS: to address this issue, we have investigated the levels of epigenetic regulation in well characterized populations of pluripotent embryonic stem cells (ESC) and multipotent adult stem cells (ASC) at the trancriptome, methylome, histone modification and microRNA levels. Differences in gene expression profiles allowed classification of stem cells into three separate populations including ESC, multipotent adult progenitor cells (MAPC) and mesenchymal stromal cells (MSC). The analysis of the PcG repressive marks, histone modifications and gene promoter methylation of differentiation and pluripotency genes demonstrated that stem cell populations with a wider differentiation potential (ESC and MAPC) showed stronger representation of epigenetic repressive marks in differentiation genes and that this epigenetic signature was progressively lost with restriction of stem cell potential. Our analysis of microRNA established specific microRNA signatures suggesting specific microRNAs involved in regulation of pluripotent and differentiation genes. CONCLUSIONS/SIGNIFICANCE: Our study leads us to propose a model where the level of epigenetic regulation, as a combination of DNA methylation and histone modification marks, at differentiation genes defines degrees of differentiation potential from progenitor and multipotent stem cells to pluripotent stem cells.

Novel genomic alterations and mechanisms associated with tumor progression in oligodendroglioma and mixed oligoastrocytoma.

Combined 1p/19q deletions are very prevalent in oligodendrogliomas (OGs) and, to a lesser extent, in oligoastrocytomas (OAs). These losses are associated with responsiveness to therapy. Using array-based comparative genomic hybridization, we screened for recurrent genomic alterations in OG and oligoastrocytoma subtypes on chromosome 19. Concomitant 1p/19q loss was detected in most of the tumors with allelic loss, but array-based comparative genomic hybridization revealed some tumors to have unrelated 1p/19q arm losses, suggesting alternative mechanisms of loss to that related to the reported t(1;19) translocation. Analyses of 1p/19q loss by fluorescence in situ hybridization and loss of heterozygosity assays and correlations of genomic data with the Ki-67 proliferation marker were also performed. Four 1q (or 19p) and 2 1p (or 19q) fluorescence in situ hybridization probe signals together with homozygosity of the 1p/19q microsatellites suggested a hypothetical mechanism of genome duplication consecutive to the loss of the derivative chromosome der(1p;19q) from the t(1;19)(1q;19p) translocation. This genome duplication was frequent in high-grade OGs and was strongly correlated with Ki-67 expression; thus, it could be related to tumor progression. Finally, in addition to the frequent 1p/19q loss, we report a novel 17q amplified region in OGs with BIRC5 as one of the possible candidate target genes of the amplicon.

The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer.

The natural history of cancers associated with virus exposure is intriguing, since only a minority of human tissues infected with these viruses inevitably progress to cancer. However, the molecular reasons why the infection is controlled or instead progresses to subsequent stages of tumorigenesis are largely unknown. In this article, we provide the first complete DNA methylomes of double-stranded DNA viruses associated with human cancer that might provide important clues to help us understand the described process. Using bisulfite genomic sequencing of multiple clones, we have obtained the DNA methylation status of every CpG dinucleotide in the genome of the Human Papilloma Viruses 16 and 18 and Human Hepatitis B Virus, and in all the transcription start sites of the Epstein-Barr Virus. These viruses are associated with infectious diseases (such as hepatitis B and infectious mononucleosis) and the development of human tumors (cervical, hepatic, and nasopharyngeal cancers, and lymphoma), and are responsible for 1 million deaths worldwide every year. The DNA methylomes presented provide evidence of the dynamic nature of the epigenome in contrast to the genome. We observed that the DNA methylome of these viruses evolves from an unmethylated to a highly methylated genome in association with the progression of the disease, from asymptomatic healthy carriers, through chronically infected tissues and pre-malignant lesions, to the full-blown invasive tumor. The observed DNA methylation changes have a major functional impact on the biological behavior of the viruses.

Translocation detection in lymphoma diagnosis by split-signal FISH: a standardised approach.

Lymphomas originating from the lymphatic system comprise about 30 entities classified according to the World Health Organization (WHO). The histopathological diagnosis is generally considered difficult and prone to mistakes. Since non-random chromosomal translocations are specifically involved in different lymphoma entities, their detection will be increasingly important. Hence, a split-signal fluorescence in situ hybridisation (FISH) procedure would be helpful in discriminating the most difficult classifications. The Euro-FISH programme, a concerted action of nine European laboratories, has validated a robust, standardised protocol to improve the diagnostic approach on lymphoma entities. Therefore, 16 fluorescent probes and 10 WHO entities, supplemented with reactive cases, were selected. The results of the Euro-FISH programme show that all probes were correctly cytogenetically located, that the standardised protocol is robust, resulting in reliable results in approximately 90% of cases, and that the procedure could be implemented in every laboratory, bringing the relatively easy interpretation of split-signal probes within the reach of many pathology laboratories.

Expression of CYP3A4 as a predictor of response to chemotherapy in peripheral T-cell lymphomas.

Peripheral T-cell lymphomas (PTCLs) are aggressive tumors in which the current therapy based on multiagent chemotherapy is not successful. Since cytochrome P450 3A subfamily (CYP3A) enzymes are involved in the inactivation of chemotherapy drugs, we hypothesized that CYP3A and P-glycoprotein (MDR1) expression in these lymphomas could result in a poor clinical response. We measured tumoral CYP3A and MDR1 mRNA content in 44 T-cell lymphomas, finding a large variation in CYP3A expression. Multiplex polymerase chain reaction (PCR) analysis and fluorescence in situ hybridization (FISH) analysis showed genomic gains affecting CYP3A and MDR1 genes in T-cell lines and primary tumors, suggesting that this could be the mechanism underlying the tumoral expression variation. To test whether the tumoral expression of CYP3A and/or MDR1 could influence PTCL treatment outcome, their expression levels were compared with the clinical response and survival of the patients, finding that a high tumoral expression of CYP3A4 was significantly associated with a lower complete remission rate. This was further investigated with cell lines stably expressing CYP3A4 that exhibited an increased resistance to doxorubicin and etoposide. In conclusion, a high CYP3A4 tumoral expression could be useful to predict poor response to the standard PTCL chemotherapy; in these cases alternative chemotherapy combinations or doses should be explored.

Generation of a new monoclonal antibody against MALT1 by genetic immunization.

Genetic immunization (GI), which is primarily used for vaccine purposes, is a method for producing antibodies to a protein by delivering the gene encoding the protein as a eukaryotic expression vector instead of the protein itself. The mucosa-associated lymphoid tissue lymphoma translocation gene 1 (MALT1) is one of the most likely candidates for involvement in pathogenesis of MALT lymphoma and probably of multiple myelomas. In the present work we describe the production and characterization of a mouse monoclonal antibody (mAb) directed against MALT1 and the study of MALT1 protein expression in a large series of lymphomas and myeloma cell lines. The full-length coding sequence of human MALT1 was inserted into pcDNA3 vector and delivered into mouse skin using a helium gene gun. Six new mAbs against the MALT1 molecule were produced. In order to characterize and confirm the specificity of these mAbs, Western blot (WB) and immunoprecipitation (IP) analyses were performed. A new anti-MALT1 mAb was selected and tested in a large series of cell lines. These results confirm that GI is a reliable and effective alternative method for production of mAbs, allowing accurate and sensitive detection and screening of proteins by WB.

Primary Ewing sarcoma of the tentorium presenting with intracranial hemorrhage in a child.

Spontaneous intracerebral hemorrhage in children is usually related to cerebrovascular conditions. Brain tumors presenting with spontaneous bleeding account for approximately 10% of intracranial hemorrhages in children. The occurrence of primitive central nervous system lesions in the Ewing sarcoma family of tumors (ESFT) not related to bone or metastatic disease is a rare condition. The authors report on a child who presented with intracranial bleeding secondary to a nonmetastatic tentorial ESFT confirmed by detection of the fusion gene EWS-ERG. A detailed review of the literature reveals that most primary intracranial ESFT had a meningeal attachment, and that almost half of them presented at diagnosis with hemorrhage. Distinguishing between ESFT and other intracranial neoplasms is essential because the treatment and prognosis differ remarkably from that of other tumors, namely central primitive neuroectodermal tumors (PNETs). Whereas adjuvant treatment for ESFT consists of local or regional radiotherapy and chemotherapy containing alkylating agents, central PNETs are generally treated with whole neuraxis radiation and platinum-based chemotherapy. Additionally, the prognosis for intracranial ESFT might be better than the one for nonpineal central PNETs.