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Using genomics to define pediatric blood cancers and inform practice.

ABSTRACT: Over the past decade, there has been exponential growth in the number of genome sequencing studies performed across a spectrum of human diseases as sequencing technologies and analytic pipelines improve and costs decline. Pediatric hematologic malignancies have been no exception, with a multitude of next generation sequencing studies conducted on large cohorts of patients in recent years. These efforts have defined the mutational landscape of a number of leukemia subtypes and also identified germ-line genetic variants biologically and clinically relevant to pediatric leukemias. The findings have deepened our understanding of the biology of many childhood leukemias. Additionally, a number of recent discoveries may positively impact the care of pediatric leukemia patients through refinement of risk stratification, identification of targetable genetic lesions, and determination of risk for therapy-related toxicity. Although incredibly promising, many questions remain, including the biologic significance of identified genetic lesions and their clinical implications in the context of contemporary therapy. Importantly, the identification of germ-line mutations and variants with possible implications for members of the patient's family raises challenging ethical questions. Here, we review emerging genomic data germane to pediatric hematologic malignancies.

SUBMITTER: Rau RE

PROVIDER: S-EPMC6245969 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Using genomics to define pediatric blood cancers and inform practice.

Rau Rachel E RE Loh Mignon L ML

Hematology. American Society of Hematology. Education Program 20181101 1

Over the past decade, there has been exponential growth in the number of genome sequencing studies performed across a spectrum of human diseases as sequencing technologies and analytic pipelines improve and costs decline. Pediatric hematologic malignancies have been no exception, with a multitude of next generation sequencing studies conducted on large cohorts of patients in recent years. These efforts have defined the mutational landscape of a number of leukemia subtypes and also identified ger ...[more]

PMID: 30504323

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Project description:BackgroundIn the United Kingdom, healthcare data is collected on all patients receiving National Health Service (NHS) care, including children and young people (CYP) with cancer. This data is used to inform service delivery, and with special permissions used for research. The use of routinely collected health data in research is an advancing field with huge potential benefit, particularly in CYP with cancer where case numbers are small and the impact across the life course can be significant. Patient and public involvement (PPI) exercise aims: Identify current barriers to trust relating to the use of healthcare data for research. Determine ways to increase public and patient confidence in the use of healthcare data in research. Define areas of research importance to CYP and their carers using healthcare data.MethodsYoung people currently aged between 16 and 25 years who had a cancer diagnosis before the age of 20 years and carers of a young person with cancer were invited to take part via social media and existing networks of service users. Data was collected during two interactive online workshops totalling 5 h and comprising of presentations from health data experts, case-studies and group discussions. With participant consent the workshops were recorded, transcribed verbatim and analysed using thematic analysis.ResultsTen young people and six carers attended workshop one. Four young people and four carers returned for workshop two. Lack of awareness of how data is used, and negative media reporting were seen as the main causes of mistrust. Better communication and education on how data is used were felt to be important to improving public confidence. Participants want the ability to have control over their own data use. Late effects, social and education outcomes and research on rare tumours were described as key research priorities for data use.ConclusionsIn order to improve public and patient trust in our use of data for research, we need to improve communication about how data is used and the benefits that arise.

Project description:Rationale & objectiveThe etiology of kidney disease remains unknown in many individuals with chronic kidney disease (CKD). We created the Mayo Clinic Nephrology Genomics Clinic to improve our ability to integrate genomic and clinical data to identify the etiology of unexplained CKD.Study designRetrospective study.Setting & participantsAn essential component of our program is the Nephrology Genomics Board which consists of nephrologists, geneticists, pathologists, translational omics scientists, and trainees who interpret the patient's clinical and genetic data. Since September 2016, the Board has reviewed 163 cases (15 cystic, 100 glomerular, 6 congenital anomalies of kidney and urinary tract (CAKUT), 20 stones, 15 tubulointerstitial, and 13 other).Analytical approachTesting was performed with targeted panels, single gene analysis, or analysis of kidney-related genes from exome sequencing. Variant classification was obtained based on the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines.ResultsA definitive genetic diagnosis was achieved for 50 families (30.7%). The highest diagnostic yield was obtained in individuals with tubulointerstitial diseases (53.3%), followed by congenital anomalies of the kidney and urological tract (33.3%), glomerular (31%), cysts (26.7%), stones (25%), and others (15.4%). A further 20 (12.3%) patients had variants of interest, and variant segregation, and research activities (exome, genome, or transcriptome sequencing) are ongoing for 44 (40%) unresolved families.LimitationsPossible overestimation of diagnostic rate due to inclusion of individuals with variants with evidence of pathogenicity but classified as of uncertain significance by the clinical laboratory.ConclusionsIntegration of genomic and research testing and multidisciplinary evaluation in a nephrology cohort with CKD of unknown etiology or suspected monogenic disease provided a diagnosis in a third of families. These diagnoses had prognostic implications, and often changes in management were implemented.

Project description: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.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.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.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.

Dataset Information

Using genomics to define pediatric blood cancers and inform practice.

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Using genomics to define pediatric blood cancers and inform practice.

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