Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing.

Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. Here, we used a three-platform sequencing approach, including whole-genome sequencing (WGS), whole-exome sequencing (WES), and RNA sequencing (RNA-seq), to examine tumor and germline genomes from 309 prospectively identified children with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type. Eighty-six percent of patients harbored diagnostic (53%), prognostic (57%), therapeutically relevant (25%), and/or cancer-predisposing (18%) variants. Inclusion of WGS enabled detection of activating gene fusions and enhancer hijacks (36% and 8% of tumors, respectively), small intragenic deletions (15% of tumors), and mutational signatures revealing of pathogenic variant effects. Evaluation of paired tumor-normal data revealed relevance to tumor development for 55% of pathogenic germline variants. This study demonstrates the power of a three-platform approach that incorporates WGS to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers. SIGNIFICANCE: Pediatric cancers are driven by diverse genomic lesions, and sequencing has proven useful in evaluating high-risk and relapsed/refractory cases. We show that combined WGS, WES, and RNA-seq of tumor and paired normal tissues enables identification and characterization of genetic drivers across the full spectrum of pediatric cancers. This article is highlighted in the In This Issue feature, p. 2945.

Knowledge Is Power: Benefits, Risks, Hopes, and Decision-Making Reported by Parents Consenting to Next-Generation Sequencing for Children and Adolescents with Cancer.

OBJECTIVES: To qualitatively describe parent perspectives of next-generation genomic sequencing (NGS) for their children with cancer, including perceived benefits, risks, hopes/expectations, and decision-making process when consenting or not consenting to NGS and prior to result disclosure. DATA SOURCES: Qualitative interviews were used. CONCLUSION: Altruism is an important factor in parents consenting to NGS testing, as well as making sense of their child's cancer and legacy building. Parents described realistic hopes and expectations associated with NGS participation. Although parents endorsed the likelihood of no medical benefit, those consenting to NGS felt there was no reason not to participate. Parents declining participation expressed avoidance of worry and parent guilt if a germline variant were to be disclosed. IMPLICATIONS FOR NURSING PRACTICE: As NGS evolves into a component of the routine diagnostic workup for pediatric cancer patients, genetic nurses play a role in conducting informed consent conversations and ensuring that patients and families have realistic hopes and expectations associated with NGS.

Creating a cancer genomics curriculum for pediatric hematology-oncology fellows: A national needs assessment.

BACKGROUND: With the advent of next generation sequencing, tumor and germline genomic testing are increasingly being used in the management of pediatric cancer patients. Despite this increase in testing, many pediatric hematology-oncology (PHO) providers are not confident interpreting or utilizing tumor or germline genomic results to care for their patients. METHODS: We developed and delivered a needs assessment survey to PHO program directors, attendings, and fellows in the United States to understand this deficiency, gather data on existing cancer genomics educational initiatives, and query preferences for creating a future curriculum. RESULTS: The survey includes 31 (41%) of 74 invited PHO program directors, 110 (11%) of 1032 invited attendings, and 79 fellows. The majority of attending physicians and fellows responding to the survey agree that understanding tumor (95% attending physicians; 95% fellows) and germline (86% attending physicians; 94% fellows) genomic information is essential for their practice. However, only 9 of 31 (29%) responding programs report that they have an existing cancer genomics curriculum. Most program directors indicated that the ideal genomics curriculum would occur during the first year of fellowship and incorporate direct patient care, online modules, and problem-based learning. Attending physicians and fellows identified that addressing indications for ordering tumor and germline genomic testing, counseling about the risks and benefits of such testing, and interpreting and individualizing clinical management based on tumor and germline results should be included in a future curriculum. CONCLUSION: The results of this study reveal a great need to develop a curriculum that can be offered across PHO fellowship programs to expand knowledge in the area of cancer genomics.

Amphotericin B Penetrates into the Central Nervous System Through Focal Disruption of the Blood Brain Barrier in Experimental Hematogenous Candida Meningoencephalitis.

Hematogenous Candida meningoencephalitis (HCME) is a life-threatening complication of neonates and immunocompromised children. Amphotericin B (AmB) shows poor permeability and low cerebrospinal fluid (CSF) concentrations, but is effective in treatment of HCME. In order to better understand the mechanism of CNS penetration of AmB, we hypothesized that AmB may achieve focally higher concentrations in infected CNS lesions. An in vitro BBB model was serially infected with C. albicans. Liposomal AmB (LAMB) or deoxycholate AmB (DAMB) at 5 µg/ml were then provided, vascular and CNS compartments were sampled 4h later. For in vivo correlation, rabbits with experimental HCME received a single dose of DAMB 1 mg/kg or LAMB 5 mg/kg, and were euthanized after 1, 3, 6 and 24h. Evans blue solution (2%) 2 ml/kg administered IV one hour prior to euthanasia stained infected regions of tissue but not histologically normal areas. AmB concentrations in stained and unstained tissue regions were measured using UPLC. For selected rabbits, MRI scans performed on days 1-7 postinoculation were acquired before and after IV bolus Gd-DTPA at 15min intervals through 2h post-injection. The greatest degree of penetration of DAMB and LAMB through the in vitro BBB occurred after 24h of exposure (P=0.0022). In vivo the concentrations of LAMB and DAMB in brain abscesses were 4.35±0.59 and 3.14±0.89-times higher vs. normal tissue (P≤0.019). MRI scans demonstrated that Gd-DTPA accumulated in infected areas with disrupted BBB. Localized BBB disruption in HCME allows high concentrations of AmB within infected tissues, despite the presence of low CSF concentrations.

Speaking genomics to parents offered germline testing for cancer predisposition: Use of a 2-visit consent model.

BACKGROUND: Patients with cancer are increasingly offered genomic sequencing, including germline testing for cancer predisposition or other disorders. Such testing is unfamiliar to patients and families, and clear communication is needed to introduce genomic concepts and convey risk and benefit information. METHODS: Parents of children with cancer were offered the opportunity to have their children's tumor and germline examined with clinical genomic sequencing. Families were introduced to the study with a 2-visit informed consent model. Baseline genetic knowledge and self-reported literacy/numeracy were collected before a study introduction visit, during which basic concepts related to genomic sequencing were discussed. Information was reinforced during a second visit, during which informed consent was obtained and a posttest was administered. RESULTS: As reflected by the percentage of correct answers on the pretest and posttest assessments, this model increased genetic knowledge by 11.1% (from 77.8% to 88.9%; P < .0001) in 121 parents participating in both the study introduction and consent visits. The percentage of parents correctly identifying the meaning of somatic and germline mutations increased significantly (from 18% to 59% [somatic] and from 31% to 64% [germline]; P < .0001). Nevertheless, these concepts remained unfamiliar to one-third of the parents. No relation was identified between the change in the overall percentage of correct answers and self-reported literacy, numeracy, or demographics. CONCLUSIONS: The use of a 2-visit communication model improved knowledge of concepts relevant to genomic sequencing, particularly differences between somatic and germline testing; however, these areas remained confusing to many participants, and reinforcement may be necessary to achieve complete understanding.

Parent-child communication surrounding genetic testing for Li-Fraumeni syndrome: Living under the cloud of cancer.

BACKGROUND: Advances in the application of genetic technologies reveal a growing number of heritable disorders associated with an increased risk to develop cancer during childhood. As genetic testing is increasingly employed in the clinical setting, it is essential to understand whether parents communicate with their children about test results and to elucidate the factors that influence the content and outcomes of these conversations. METHODS: Semistructured interviews were conducted with 14 parents whose children tested positive for Li-Fraumeni syndrome (LFS). Semantic content analysis was performed on transcribed interviews, focusing on questions related to parent-child conversations about the genetic testing process and disclosure of positive test results. RESULTS: All parents emphasized the importance of involving children in conversations about LFS. The majority (93%) identified as being part of "cancer families" in which prior experiences with cancer created opportunities for communication. While all had spoken with their children about cancer, only seven (50%) specifically disclosed to their children that they had tested positive for LFS. The most common reason cited for nondisclosure at the time of this study was the young age of the children. CONCLUSION: Parents of children with LFS desire open conversations about genetic testing and cancer risk. These conversations are challenging yet essential to enable child understanding of genetic risk status and enhance compliance with health-promoting and cancer surveillance measures. Development of age-appropriate educational materials and novel clinical models to facilitate parent-child conversations about genetic test results and risk status for cancer are needed.

Ethical considerations surrounding germline next-generation sequencing of children with cancer.

INTRODUCTION: The advent of next-generation sequencing (NGS) has introduced an exciting new era in biomedical research. NGS forms the foundation of current genetic testing approaches, including targeted gene panel testing, as well as more comprehensive whole-exome and whole-genome sequencing. Together, these approaches promise to provide critical insights into the understanding of health and disease. However, with NGS testing come many ethical questions and concerns, particularly when testing involves children. These concerns are especially relevant for children with cancer, where the testing of tumor and germline tissues is increasingly being incorporated into clinical care. Areas covered: In this manuscript, we explore the key ethical considerations related to conducting germline NGS testing in pediatric oncology, focusing on the four main principles of beneficence, non-maleficence, autonomy and justice. Expert commentary: The ethical issues surrounding germline NGS testing are complex and result in part from our limited understanding of the medical relevance of many of the results obtained and poor knowledge of the impacts of testing, both beneficial and detrimental, on patients and their families. In this article we discuss the risks and benefits of germline NGS testing and the arguments for and against such testing in children with cancer.

Integrating next-generation sequencing into pediatric oncology practice: An assessment of physician confidence and understanding of clinical genomics.

BACKGROUND: The incorporation of genomic testing to identify targetable somatic alterations and predisposing germline mutations into the clinical setting is becoming increasingly more common. Despite its potential usefulness, to the authors' knowledge physician confidence with regard to understanding and applying genomic testing remains unclear, particularly within the realm of pediatric oncology. METHODS: Before initiating an institutional feasibility study regarding the integration of clinical genomic testing, the authors surveyed pediatric oncologists regarding their confidence around understanding of genomic testing, perceived usefulness of test results, preferences around the disclosure of germline test results, and possible risks and benefits of testing. RESULTS: Among survey respondents (52 of 88 contacted; response rate of 59%), only a minority were confident in interpreting, using, and discussing somatic (35%) or germline (27%) genomic test results. Providers who were confident in interpreting somatic results were significantly more likely to anticipate using the results to plan the treatment of patients with relapsed or refractory cancers (P = .009). Similarly, providers who reported confidence in interpreting germline results were significantly more likely to discuss and use these results as part of clinical care (P<.0001). The majority of physicians (93%), regardless of their level of confidence, wanted to speak to a genetic counselor before disclosing germline test results. CONCLUSIONS: Among physicians at a comprehensive pediatric cancer center, confidence in the interpretation, use, and discussion of oncology-based genomic test results appears to be low, both in terms of somatic and germline testing. To optimize the integration of genomic sequencing into cancer care, methods must be developed to improve basic competencies around cancer-based genomic testing. Given the complexities surrounding variant interpretation and genotype-phenotype relationships, interdisciplinary collaborations are warranted. Cancer 2017;123:2352-2359. © 2017 American Cancer Society.

Li-Fraumeni syndrome: a paradigm for the understanding of hereditary cancer predisposition.

Li-Fraumeni syndrome (LFS) is a rare cancer predisposing condition caused by germline mutations in TP53, the gene encoding the TP53 transcription factor. LFS is typified by the development of a wide spectrum of childhood and adult-onset malignancies, which includes, among others, the lymphoid and myeloid leukaemias, myelodysplastic syndrome and, to a lesser extent, lymphoma. Accordingly, it is important that haematologists/oncologists be familiar with this pleiotropic hereditary cancer syndrome. The high cancer risk and variability in type and age of cancer onset have raised questions about the underlying biology and optimal treatment approaches for individuals with LFS. Since its description almost 50 years ago, many clinical and basic research investigations have provided insights into the pathogenesis, manifestations, genetic testing and management strategies for individuals with LFS. Here we provide an update on the current state of knowledge regarding LFS with an emphasis, where possible, on information relevant to practicing haematologists.

Decreased infection-related mortality and improved survival in severe aplastic anemia in the past two decades.

BACKGROUND: Persistent neutropenia associated with severe aplastic anemia (SAA) is an important risk factor for development of life-threatening infections. Earlier studies underscored the high mortality associated with invasive fungal infections (IFIs) in SAA. However, little is known about the current patterns of infections and the impact of advances in anti-infective therapy on survival in SAA. METHODS: We reviewed the records of 174 patients with SAA admitted to the Hematology Branch at NHLBI from 1989 to 2008 who were unresponsive to initial immunosuppressive therapy (IST) at 6 months. Three patient groups determined by IST protocol and time interval were compared: group 1 (43 patients; December 1989-October 1996), group 2 (51 patients; November 1996-October 2002), and group 3 (80 patients; November 2002-April 2008). Outcome variables included infections, patterns of resistance, survival, and infection-related mortality. RESULTS: During the past 2 decades, infection-related mortality decreased from 37% in group 1 to 11% in group 3 (P < .001), and the frequency of IFIs decreased from 49% in group 1 to 8% in group 3 (P < .001). Overall 5-year survival for all patients (n = 420) increased from 64% in group 1 to 79% in group 3 (P < .001). Among non-responders (n = 174), it increased from 23% in group 1 to 57% in group 3 (P < .001). In multivariate analysis, younger age, absolute neutrophil count > 200 cells/µL before IST, absence of IFIs, and use of voriconazole were independently predictive of survival. CONCLUSION: During the past 2 decades, there has been a significant decrease in IFIs, infection-related mortality, and overall mortality in patients with SAA unresponsive to initial IST.

Infections in patients with aplastic anemia.

Infection is a major cause of death in patients with aplastic anemia (AA). There are differences between the immunocompromised state of a patient with AA and the patient who is neutropenic due to chemotherapy and this leads to a difference in the infections that they incur. Prolonged neutropenia is one of the largest risk factors for the development of infections with the invasive mycoses and bacteria. Recovery from neutropenia is directly related to survival, and supportive care plays a large role in protection while the patient is in a neutropenic state. The most common invasive mycoses include the Aspergillus species, Zygomycetes, Candida spp., and Fusarium spp. Bacterial infections that are seen in patients with AA include gram-positive coagulase-negative Staphylococcus species, Enterococcus, Staphylococus aureus, Clostridium spp., Micrococcus, alpha-hemolytic streptococci, Listeria monocytogenes, and Bacillus cereus. Gram-negative infections including gram-negative bacilli, Escherichia coli, Salmonella, Bacteroides fragilis, Klebsiella oxytoca, Klebsiella pneumonia, Aeromonas hydrophilia, Pseudomonas aeruginosa, and Vibrio vulnificus. Viral infections are much less common but include those that belong to the Herpesviridae family, community-acquired respiratory viral infection, and the viral hepatitides A, B, and C. Evidence of the parasite Strongyloides stercoralis has also been documented. This review discusses the major invasive fungal infections, bacterial pathogens, parasites, and viral infections that are found in patients with AA who are treated with immunosuppressive therapy. The specific immune impairment and current treatment parameters for each of these classes of infection will also be discussed.

Trans fatty acids and conjugated linoleic acids in the milk of urban women and nomadic Fulani of northern Nigeria.

BACKGROUND: Trans fatty acids (TFAs) and conjugated linoleic acids (CLAs) are present in dairy products and human milk and can have detrimental and beneficial effects in humans. The content of TFAs and CLAs in milk is determined largely by the diet of the mother. METHODS: We compared the proportions of TFAs and CLAs in the milk of rural Fulani in northern Nigeria who consume dairy products to that of women living in an urban center who consume little in the way of dairy products. Lactating Fulani women (n=41) and women residing in the city of Jos, Nigeria (n=41) were recruited into the study. We predicted that the milk of the Fulani pastoralists would contain higher amounts of TFAs and CLAs compared to their urban counterparts. RESULTS: The mean total TFA proportions for the Fulani and urban women were 0.22% and 0.34%, respectively, and were not significantly different. The percentages of CLAs in milk fat were not different between rural and urban women (0.16% vs 0.14%). These TFA and CLA values were 4- to 10-fold lower than for milk of women elsewhere in the world. CONCLUSIONS: The percentages of TFAs and CLAs in milk were not different between rural and urban dwellers in northern Nigeria whose diets differ greatly in the amounts of dairy products they contain. However, the fact that the percentages of TFAs and CLAs in the milk of Nigerian women were much lower than the percentages reported from other parts of the world may have implications for the long-term growth and development of infants in the northern Nigeria and elsewhere in the Western Sahel.