Germline genomic findings in children and young adults with melanocytic tumors.

In this retrospective study, we examined the prevalence and spectrum of germline variants in selected cancer predisposition genes in 38 children and young adults with melanocytic lesions at St. Jude Children's Research Hospital. Diagnoses included malignant melanoma (n = 16; 42%), spitzoid melanoma (n = 16; 42%), uveal melanoma (n = 5; 13%), and malignant melanoma arising in a giant congenital melanocytic nevus (n = 1; 3%). Six patients (15.8%) harbored pathogenic germline variants: one with bi-allelic PMS2 variants, one with a heterozygous 17q21.31 deletion, and one each with a pathogenic variant in TP53, BRIP1, ATM, or AXIN2. Overall, 15.8% of patients harbored a cancer-predisposing genetic variant.

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.

Germline Mutations in Predisposition Genes in Pediatric Cancer.

BACKGROUND: The prevalence and spectrum of predisposing mutations among children and adolescents with cancer are largely unknown. Knowledge of such mutations may improve the understanding of tumorigenesis, direct patient care, and enable genetic counseling of patients and families. METHODS: In 1120 patients younger than 20 years of age, we sequenced the whole genomes (in 595 patients), whole exomes (in 456), or both (in 69). We analyzed the DNA sequences of 565 genes, including 60 that have been associated with autosomal dominant cancer-predisposition syndromes, for the presence of germline mutations. The pathogenicity of the mutations was determined by a panel of medical experts with the use of cancer-specific and locus-specific genetic databases, the medical literature, computational predictions, and second hits identified in the tumor genome. The same approach was used to analyze data from 966 persons who did not have known cancer in the 1000 Genomes Project, and a similar approach was used to analyze data from an autism study (from 515 persons with autism and 208 persons without autism). RESULTS: Mutations that were deemed to be pathogenic or probably pathogenic were identified in 95 patients with cancer (8.5%), as compared with 1.1% of the persons in the 1000 Genomes Project and 0.6% of the participants in the autism study. The most commonly mutated genes in the affected patients were TP53 (in 50 patients), APC (in 6), BRCA2 (in 6), NF1 (in 4), PMS2 (in 4), RB1 (in 3), and RUNX1 (in 3). A total of 18 additional patients had protein-truncating mutations in tumor-suppressor genes. Of the 58 patients with a predisposing mutation and available information on family history, 23 (40%) had a family history of cancer. CONCLUSIONS: Germline mutations in cancer-predisposing genes were identified in 8.5% of the children and adolescents with cancer. Family history did not predict the presence of an underlying predisposition syndrome in most patients. (Funded by the American Lebanese Syrian Associated Charities and the National Cancer Institute.).

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.

Influence of anchoring on miscarriage risk perception associated with amniocentesis.

One factor women consider when deciding whether to pursue amniocentesis is the risk of miscarriage. People use mechanisms like anchoring, or the prior belief regarding the magnitude of risk, as a frame of reference for new information. This study aimed to determine a woman's perception of miscarriage risk associated with amniocentesis before and after genetic counseling and to determine what factors anchor a woman's perception of miscarriage risk. One hundred thirteen women being seen for prenatal genetic counseling and possible amniocentesis at six Houston clinics participated in the two-part anonymous survey. While most women (56.7 %) perceived the risk as low or average pre-counseling and indicated the numeric risk of amniocentesis as <1 %, significantly more patients (73 %) correctly identified the numeric risk as <1 % post-counseling (p < 0.0001). However, the majority of patients' qualitative risk perception did not change after the genetic counseling session (60 %). Those who changed their feeling about the risk after counseling showed a decreased perception of the risk (p < 0.0001). Participants who elected amniocentesis had a significantly lower perception of the risk (p = 0.017) whereas those who declined amniocentesis were more likely to view the risk as high (p = 0.004). The only two anchoring factors that had an effect were having a friend or relative with a personal or family history of a genetic disorder (p = 0.001) and having a child already (p = 0.038); both were associated with a lower risk perception. The lack of significant factors may reflect the uniqueness of each patient's risk assessment framework and reinforces the importance of genetic counseling to elucidate individual concerns, particularly as non-invasive prenatal testing becomes more widely available and further complicates the prenatal testing landscape.

Pathogenic Variants in Adult-Onset Cancer Predisposition Genes in Pediatric Cancer: Prevalence and Impact on Tumor Molecular Features and Clinical Management.

PURPOSE: Clinical genomic sequencing of pediatric tumors is increasingly uncovering pathogenic variants in adult-onset cancer predisposition genes (aoCPG). Nevertheless, it remains poorly understood how often aoCPG variants are of germline origin and whether they influence tumor molecular profiles and/or clinical care. In this study, we examined the prevalence, spectrum, and impacts of aoCPG variants on tumor genomic features and patient management at our institution. EXPERIMENTAL DESIGN: This is a retrospective study of 1,018 children with cancer who underwent clinical genomic sequencing of their tumors. Tumor genomic data were queried for pathogenic variants affecting 24 preselected aoCPGs. Available tumor whole-genome sequencing (WGS) data were evaluated for second hit mutations, loss of heterozygosity (LOH), DNA mutational signatures, and homologous recombination deficiency (HRD). Patients whose tumors harbored one or more pathogenic aoCPG variants underwent subsequent germline testing based on hereditary cancer evaluation and family or provider preference. RESULTS: Thirty-three patients (3%) had tumors harboring pathogenic variants affecting one or more aoCPGs. Among 21 tumors with sufficient WGS sequencing data, six (29%) harbored a second hit or LOH affecting the remaining aoCPG allele with four of these six tumors (67%) also exhibiting a DNA mutational signature consistent with the altered aoCPG. Two additional tumors demonstrated HRD, of uncertain relation to the identified aoCPG variant. Twenty-one of 26 patients (81%) completing germline testing were positive for the aoCPG variant in the germline. All germline-positive patients were counseled regarding future cancer risks, surveillance, and risk-reducing measures. No patients had immediate cancer therapy changed due to aoCPG data. CONCLUSIONS: AoCPG variants are rare in pediatric tumors; however, many originate in the germline. Almost one third of tumor aoCPG variants examined exhibited a second hit and/or conferred an abnormal DNA mutational profile suggesting a role in tumor formation. aoCPG information aids in cancer risk prediction but is not commonly used to alter the treatment of pediatric cancers.

Parent Quality of Life After Disclosure of Pediatric Oncology Germline Sequencing Results.

PURPOSE: To characterize parents' quality of life (QoL) after germline genomic sequencing for their children with cancer. METHODS: Participants were n = 104 parents of children with cancer enrolled in a prospective study of clinical tumor and germline genomic sequencing. Parents completed surveys at study consent (T0), before disclosure of their child's germline results (T1), and again ≥5 weeks after results disclosure (T2). Bivariate associations with QoL were examined, followed by a multivariable regression model predicting parents' psychological distress. RESULTS: At T2, parental distress significantly differed by their children's germline result type (positive, uncertain, negative; P = .038), parent relationship status (P = .04), predisclosure genetics knowledge (P = .006), and predisclosure worry about sequencing (P < .001). Specifically, parents of children with positive (ie, pathogenic or likely pathogenic) results experienced greater distress than those of children with negative results (P = .029), as did parents who were single, more knowledgeable about genetics, and with greater worry. In the adjusted regression model, a positive germline result remained significantly associated with parents' lower QoL at T2 follow-up (F [4,92] = 9.95; P < .001; R2 = .30; ß = .19; P = .031). CONCLUSION: Germline genomic sequencing for children with cancer is associated with distress among parents when revealing an underlying cancer predisposition among their affected children. Genetic education and counseling before and after germline sequencing may help attenuate this impact on QoL by addressing parents' concerns about test results and their health implications. Assessing parents' worry early in the testing process may also aid in identifying those most likely in need of psychosocial support.

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.

Factors Associated with Declining to Participate in a Pediatric Oncology Next Generation Sequencing Study.

PURPOSE: For the advances of pediatric oncology next generation sequencing (NGS) research to equitably benefit all children, a diverse and representative sample of participants is needed. However, little is known about demographic and clinical characteristics that differentiate families who decline enrollment in pediatric oncology NGS research. METHODS: Demographic and clinical data were retrospectively extracted for 363 pediatric oncology patients (0-21 years) approached for enrollment on Genomes for Kids (G4K), a study examining the feasibility of comprehensive clinical genomic analysis of tumors and paired normal samples. Demographic and clinical factors that significantly differentiated which families declined were subsequently compared to enrollment in Clinical Implementation of Pharmacogenetics (PG4KDS) for 348 families, a pharmacogenomics study with more explicit therapeutic benefit examining genes affecting drug responses and metabolism. RESULTS: Fifty-three (14.6%) families declined enrollment in G4K. Race/ethnicity was the only variable that significantly differentiated study refusal using multivariate logistic regression, with families of black children more likely to decline enrollment compared to families of non-Hispanic or Hispanic white children. Reasons for declining G4K were generally consistent with other pediatric genomics research, with feeling overwhelmed and insurance discrimination fears most frequently cited. Families of black children were also more likely to decline enrollment in PG4KDS. Thirteen (3.7%) of the 348 families approached for both studies declined PG4KDS. CONCLUSION: Race/ethnicity differentiated study declination across two different pediatric oncology genomics studies, suggesting enrollment disparities in the context of pediatric oncology genomics research. Genomics research participant samples that do not fully represent racial and ethnic minorities risk further exacerbating health disparities. Additional work is needed to understand the nuances of parental decision making in genomic research and facilitate enrollment of diverse patient populations.

Enrichment of heterozygous germline RECQL4 loss-of-function variants in pediatric osteosarcoma.

Patients harboring germline pathogenic biallelic variants in genes involved in the recognition and repair of DNA damage are known to have a substantially increased cancer risk. Emerging evidence suggests that individuals harboring heterozygous variants in these same genes may also be at heightened, albeit lesser, risk for cancer. Herein, we sought to determine whether heterozygous variants in RECQL4, the gene encoding an essential DNA helicase that is defective in children with the autosomal recessive cancer-predisposing condition Rothmund-Thomson syndrome (RTS), are associated with increased risk for childhood cancer. To address this question, we interrogated germline sequence data from 4435 pediatric cancer patients at St. Jude Children's Research Hospital and 1127 from the National Cancer Institute Therapeutically Applicable Research to Generate Effective Treatment (TARGET) database and identified 24 (0.43%) who harbored loss-of-function (LOF) RECQL4 variants, including five of 249 (2.0%) with osteosarcoma (OS). These RECQL4 variants were significantly overrepresented in children with OS, the cancer most frequently observed in patients with RTS, as compared to 134,187 noncancer controls in the Genome Aggregation Database (gnomAD v2.1; P = 0.00087, odds ratio [OR] = 7.1, 95% CI, 2.9-17). Nine of the 24 (38%) individuals possessed the same c.1573delT (p.Cys525Alafs) variant located in the highly conserved DNA helicase domain, suggesting that disruption of this domain is central to oncogenesis. Altogether these data expand our understanding of the genetic factors predisposing to childhood cancer and reveal a novel association between heterozygous RECQL4 LOF variants and development of pediatric OS.

Genetic Predisposition to Neonatal Tumors.

The development of tumors within the first month of life is extremely rare and this very young age at presentation should raise concern for an underlying cancer predisposition syndrome. This chapter discusses genetic predisposition to neonatal solid tumors, specifically those involving the eyes, kidneys, liver, adrenal glands and lungs. For each tumor type, we discuss the most common associated predisposition syndromes and for eye and lung tumors, we also review the approach to diagnosis and management. The reader is referred to the other chapters of this volume for an overview of management details for the other tumor types. The management of neonates with cancer predisposing syndromes is challenging, with many patients demonstrating multisystem involvement. Accordingly, it is critical to use a team approach, where providers with expertise in neonatology, oncology, genetics, surgery and other pediatric subspecialties can appropriately tailor management of the patient and coordinate genetic evaluation of the family.