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1.
J Neurosurg Pediatr ; 31(3): 212-220, 2023 03 01.
Article in English | MEDLINE | ID: mdl-36681951

ABSTRACT

OBJECTIVE: Genetic alterations are increasingly recognized as etiologic factors linked to the pathogenesis and development of cerebrovascular anomalies. Their identification allows for advanced screening and targeted therapeutic approaches. The authors aimed to describe the role of a collaborative approach to care and genetic testing in pediatric patients with neurovascular anomalies, with the objectives of identifying what genetic testing recommendations were made, the yield of genetic testing, and the implications for familial screening and management at present and in the future. METHODS: The authors performed a descriptive retrospective cohort study examining pediatric patients genetically screened through the Pediatric Neurovascular Program of a single treatment center. Patients 18 years of age and younger with neurovascular anomalies, diagnosed radiographically or histopathologically, were evaluated for germline genetic testing. Patient demographic data and germline genetic testing and recommendation, clinical, treatment, and outcome data were collected and analyzed. RESULTS: Sixty patients were included; 29 (47.5%) were female. The mean age at consultation was 11.0 ± 4.9 years. Diagnoses included cerebral arteriovenous malformations (AVMs) (n = 23), cerebral cavernous malformations (n = 19), non-neurofibromatosis/non-sickle cell moyamoya (n = 8), diffuse cerebral proliferative angiopathy, and megalencephaly-capillary malformation. Of the 56 patients recommended to have genetic testing, 40 completed it. Genetic alterations were found in 13 (23%) patients. Four patients with AVMs had RASA1, GDF2, and ACVRL1 mutations. Four patients with cavernous malformations had Krit1 mutations. One with moyamoya disease had an RNF213 mutation. Three patients with megalencephaly-capillary malformation had PIK3CA mutations, and 1 patient with a cavernous sinus lesion had an MED12 mutation. The majority of AVM patients were treated surgically. Patients with diffuse cerebral proliferative angiopathy were treated medically with sirolimus. At-risk relatives of 3 patients positive for genetic anomalies had also been tested. CONCLUSIONS: This study demonstrates a role for exploring genetic alterations in the identification and treatment of pediatric neurovascular disease pathogenesis. Germline genetic mutations were found in almost one-quarter of the patients screened in this study, results that helped to identify medically targeted treatment modalities for some pediatric neurovascular patients. Insight into the genetic etiology of vascular anomalies may provide broader clinical implications for risk assessment, family screening, follow-up surveillance, and medical management.


Subject(s)
Intracranial Arteriovenous Malformations , Vascular Malformations , Humans , Child , Female , Adolescent , Male , Retrospective Studies , Mutation , Activin Receptors, Type II/genetics , p120 GTPase Activating Protein/genetics , Adenosine Triphosphatases/genetics , Ubiquitin-Protein Ligases/genetics
2.
Clin Dermatol ; 40(4): 313-321, 2022.
Article in English | MEDLINE | ID: mdl-35181412

ABSTRACT

One in 10 infants are born with a vascular birthmark each year. Some vascular birthmarks, such as infantile hemangiomas, are common, while vascular malformations, such as capillary, lymphatic, venous, and arteriovenous malformations, are less so. Diagnosing uncommon vascular birthmarks can be challenging, given the phenotypic heterogeneity and overlap among these lesions. Both sporadic and germline variants have been detected in various genes associated with vascular birthmarks. Identification of these genetic variants offers insight into both diagnosis and underlying molecular pathways and can be fundamental in the discovery of novel therapeutic approaches. The PIK3/AKT/mTOR and RAS/MEK/ERK signaling pathways, which mediate cell growth and angiogenesis, are activated secondary to genetic variations in vascular malformations. Somatic variants in TEK (TIE2) and PIK3CA cause venous malformations. Variants in PIK3CA also cause lymphatic malformations as well as a number of overgrowth syndromes associated with vascular anomalies. Variants in GNAQ and GNA11 have been identified in both so-called "congenital" hemangiomas and capillary malformations. RASA1 and EPHB4 variants are associated with capillary malformation-arteriovenous malformation syndrome. This review discusses the genetics of vascular birthmarks, including the various phenotypes, genetic variants, pathogenesis, associated syndromes, and new diagnostic techniques.


Subject(s)
Hemangioma , Vascular Malformations , Capillaries/abnormalities , Class I Phosphatidylinositol 3-Kinases/genetics , Hemangioma/genetics , Humans , Mitogen-Activated Protein Kinase Kinases/genetics , Mutation , Proto-Oncogene Proteins c-akt/genetics , Syndrome , TOR Serine-Threonine Kinases/genetics , Vascular Malformations/diagnosis , Vascular Malformations/genetics , Vascular Malformations/pathology , p120 GTPase Activating Protein/genetics
3.
Am J Hematol ; 96(11): 1491-1504, 2021 11 01.
Article in English | MEDLINE | ID: mdl-34342889

ABSTRACT

The North American Pediatric Aplastic Anemia Consortium (NAPAAC) is a group of pediatric hematologist-oncologists, hematopathologists, and bone marrow transplant physicians from 46 institutions in North America with interest and expertise in aplastic anemia, inherited bone marrow failure syndromes, and myelodysplastic syndromes. The NAPAAC Bone Marrow Failure Diagnosis and Care Guidelines Working Group was established with the charge of harmonizing the approach to the diagnostic workup of aplastic anemia in an effort to standardize best practices in the field. This document outlines the rationale for initial evaluations in pediatric patients presenting with signs and symptoms concerning for severe aplastic anemia.


Subject(s)
Anemia, Aplastic/diagnosis , Anemia, Aplastic/pathology , Bone Marrow/pathology , Child , Diagnosis, Differential , Fetal Hemoglobin/analysis , HLA Antigens/analysis , Humans , North America , Severity of Illness Index
4.
Mol Genet Genomic Med ; 9(12): e1685, 2021 12.
Article in English | MEDLINE | ID: mdl-33834622

ABSTRACT

BACKGROUND: Disrupted endothelial BMP9/10 signaling may contribute to the pathophysiology of both hereditary hemorrhagic telangiectasia (HHT) and pulmonary arterial hypertension (PAH), yet loss of circulating BMP9 has not been confirmed in individuals with ultra-rare homozygous GDF2 (BMP9 gene) nonsense mutations. We studied two pediatric patients homozygous for GDF2 (BMP9 gene) nonsense mutations: one with PAH (c.[76C>T];[76C>T] or p.[Gln26Ter];[Gln26Ter] and a new individual with pulmonary arteriovenous malformations (PAVMs; c.[835G>T];[835G>T] or p.[Glu279Ter];[Glu279Ter]); both with facial telangiectases. METHODS: Plasma samples were assayed for BMP9 and BMP10 by ELISA. In parallel, serum BMP activity was assayed using an endothelial BRE-luciferase reporter cell line (HMEC1-BRE). Proteins were expressed for assessment of secretion and processing. RESULTS: Plasma levels of both BMP9 and BMP10 were undetectable in the two homozygous index cases and this corresponded to low serum-derived endothelial BMP activity in the patients. Measured BMP9 and BMP10 levels were reduced in the asymptomatic heterozygous p.[Glu279Ter] parents, but serum activity was normal. Although expression studies suggested alternate translation can be initiated at Met57 in the p.[Gln26Ter] mutant, this does not result in secretion of functional BMP9. CONCLUSION: Collectively, these data show that homozygous GDF2 mutations, leading to a loss of circulating BMP9 and BMP10, can cause either pediatric PAH and/or "HHT-like" telangiectases and PAVMs. Although patients reported to date have manifestations that overlap with those of HHT, none meet the Curaçao criteria for HHT and seem distinct from HHT in terms of the location and appearance of telangiectases, and a tendency for tiny, diffuse PAVMs.


Subject(s)
Bone Morphogenetic Proteins/blood , Codon, Nonsense , Growth Differentiation Factor 2/blood , Growth Differentiation Factor 2/genetics , Homozygote , Pulmonary Arterial Hypertension/diagnosis , Pulmonary Arterial Hypertension/etiology , Telangiectasia, Hereditary Hemorrhagic/diagnosis , Telangiectasia, Hereditary Hemorrhagic/etiology , Alleles , Angiography , Cell Line , Child , Enzyme-Linked Immunosorbent Assay , Genetic Association Studies , Genetic Predisposition to Disease , Humans , Phenotype , Syndrome
5.
Hum Mutat ; 41(11): 1918-1930, 2020 11.
Article in English | MEDLINE | ID: mdl-32790018

ABSTRACT

Diamond-Blackfan anemia (DBA) is a ribosomopathy of variable expressivity and penetrance characterized by red cell aplasia, congenital anomalies, and predisposition to certain cancers, including early-onset colorectal cancer (CRC). DBA is primarily caused by a dominant mutation of a ribosomal protein (RP) gene, although approximately 20% of patients remain genetically uncharacterized despite exome sequencing and copy number analysis. Although somatic loss-of-function mutations in RP genes have been reported in sporadic cancers, with the exceptions of 5q-myelodysplastic syndrome (RPS14) and microsatellite unstable CRC (RPL22), these cancers are not enriched in DBA. Conversely, pathogenic variants in RPS20 were previously implicated in familial CRC; however, none of the reported individuals had classical DBA features. We describe two unrelated children with DBA lacking variants in known DBA genes who were found by exome sequencing to have de novo novel missense variants in RPS20. The variants affect the same amino acid but result in different substitutions and reduce the RPS20 protein level. Yeast models with mutation of the cognate residue resulted in defects in growth, ribosome biogenesis, and polysome formation. These findings expand the phenotypic spectrum of RPS20 mutation beyond familial CRC to include DBA, which itself is associated with increased risk of CRC.


Subject(s)
Anemia, Diamond-Blackfan/genetics , Germ-Line Mutation , Ribosomal Proteins/genetics , Adolescent , Amino Acid Sequence , Child , Colorectal Neoplasms/genetics , Female , Humans , Infant, Newborn , Male , Pedigree , Penetrance , Protein Structure, Tertiary , Exome Sequencing
6.
Int J Hematol ; 110(1): 95-101, 2019 Jul.
Article in English | MEDLINE | ID: mdl-30904992

ABSTRACT

Cerebral cavernous malformation 3 (CCM3) is a vascular malformation disorder causing brain slow-flow vascular parenchymal lesions. These lesions are the result of variants in the Programmed Cell Death Protein 10 (PDCD10) gene, located on 3q26.1. We report an 8-month-old patient who was presented with seizures and intracranial abscesses and was found to have a variant of PDCD10 on whole exome sequencing, representing, to our knowledge, the youngest case of CCM3 described in the literature. Her clinical course was complicated by the development of neutropenia, requiring granulocyte colony-stimulating factor, and thrombocytopenia, requiring intermittent platelet transfusions, with later development of B acute lymphoblastic leukemia 2 years after initial presentation. This case represents the first description in the literature of hematologic complications in the setting of CCM3. We hypothesize that these hematological manifestations are the result of alterations in the actin and microtubule cytoskeleton, affecting the process of hematopoiesis in a similar fashion to the documented effect of the PDCD10 variant on neuronal migration.


Subject(s)
Apoptosis Regulatory Proteins/genetics , Central Nervous System Neoplasms/complications , Hemangioma, Cavernous, Central Nervous System/complications , Membrane Proteins/genetics , Neutropenia/etiology , Proto-Oncogene Proteins/genetics , Thrombocytopenia/etiology , Central Nervous System Neoplasms/genetics , Female , Genetic Variation , Hemangioma, Cavernous, Central Nervous System/genetics , Hematopoiesis , Humans , Infant , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/etiology
8.
Pediatr Blood Cancer ; 66(1): e27439, 2019 01.
Article in English | MEDLINE | ID: mdl-30198636

ABSTRACT

Neutropenia in pediatric patients can be due to a variety of disorders. We describe two patients who underwent extensive evaluation over many years for arthralgias and moderate neutropenia of unclear etiology. Genetic testing identified a pathogenic variant in PSTPIP1 (proline-serine-threonine phosphatase-interacting protein 1) in both patients. Markedly elevated inflammatory markers and zinc levels confirmed the rare diagnosis of PSTPIP1-associated myeloid-related proteinemia inflammatory (PAMI) syndrome, tailoring treatment. Neutropenia is common in patients with PAMI syndrome. Unique mutations seen in PAMI syndrome may account for the specific phenotypic features of this disorder.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Arthralgia/pathology , Cytoskeletal Proteins/genetics , Inflammation/complications , Metal Metabolism, Inborn Errors/complications , Mutation , Neutropenia/pathology , Arthralgia/etiology , Arthralgia/genetics , Child , Female , Humans , Neutropenia/etiology , Neutropenia/genetics , Phenotype , Prognosis , Syndrome
9.
Genet Med ; 21(5): 1100-1110, 2019 05.
Article in English | MEDLINE | ID: mdl-30287922

ABSTRACT

PURPOSE: Clinical sequencing emerging in health care may result in secondary findings (SFs). METHODS: Seventy-four of 6240 (1.2%) participants who underwent genome or exome sequencing through the Clinical Sequencing Exploratory Research (CSER) Consortium received one or more SFs from the original American College of Medical Genetics and Genomics (ACMG) recommended 56 gene-condition pair list; we assessed clinical and psychosocial actions. RESULTS: The overall adjusted prevalence of SFs in the ACMG 56 genes across the CSER consortium was 1.7%. Initially 32% of the family histories were positive, and post disclosure, this increased to 48%. The average cost of follow-up medical actions per finding up to a 1-year period was $128 (observed, range: $0-$678) and $421 (recommended, range: $141-$1114). Case reports revealed variability in the frequency of and follow-up on medical recommendations patients received associated with each SF gene-condition pair. Participants did not report adverse psychosocial impact associated with receiving SFs; this was corroborated by 18 participant (or parent) interviews. All interviewed participants shared findings with relatives and reported that relatives did not pursue additional testing or care. CONCLUSION: Our results suggest that disclosure of SFs shows little to no adverse impact on participants and adds only modestly to near-term health-care costs; additional studies are needed to confirm these findings.


Subject(s)
Genetic Testing/economics , Incidental Findings , Whole Genome Sequencing/ethics , Adult , Decision Making/ethics , Disclosure , Exome , Female , Genetic Testing/ethics , Genetic Testing/standards , Genomics/methods , Health Care Costs , Health Knowledge, Attitudes, Practice , Health Personnel , High-Throughput Nucleotide Sequencing/ethics , Humans , Intention , Male , Patients , Prevalence , Whole Genome Sequencing/economics
10.
Patient Educ Couns ; 102(4): 680-686, 2019 04.
Article in English | MEDLINE | ID: mdl-30482469

ABSTRACT

OBJECTIVE: To examine communication patterns and behaviors during disclosure of exome sequencing (ES) results to parents of pediatric cancer patients, and describe common themes in parental communication. METHODS: Using mixed methods, we analyzed transcripts of sessions where parents of pediatric cancer patients received ES results from an oncologist and genetic counselor. Seventy-six transcripts were analyzed for frequency of clinician information-giving, partnering-supportive talk, and active parent participation. A subset of 40 transcripts were analyzed using thematic content analysis. RESULTS: Disclosures consisted mostly of clinician talk (84% of total talk), which was focused on providing information (62% of clinicians' utterances) with occasional partnering-supportive talk (7% of clinicians' utterances). Most parents assumed a passive, listening role (16% of total talk). Themes in parental communication included expressing relief and the significance of an answer, concern about sharing results and responsibility for inheritance, and seeking clarification of health implications of results. CONCLUSION: Our finding of low levels of active parent participation during ES disclosures highlights the need to improve patient/parent engagement and understanding in a genetic setting. PRACTICE IMPLICATIONS: Clinician communication strategies that could encourage parent participation and understanding include checking for parent understanding, partnership-building, and tailoring ES discussions to address parent concerns and preferences.


Subject(s)
Communication , Disclosure , Exome/genetics , Genetic Counseling , Neoplasms/genetics , Oncologists/psychology , Parents/psychology , Adult , Child , Decision Making , Humans , Medical Oncology , Middle Aged , Neoplasms/psychology , Patients/psychology , Physician-Patient Relations , Physicians/psychology , Professional-Family Relations
11.
Patient Educ Couns ; 102(5): 895-901, 2019 05.
Article in English | MEDLINE | ID: mdl-30581014

ABSTRACT

OBJECTIVES: To describe how linguistic tools used by interpreters during return of genomic sequencing results may have impacted communication with Spanish-speaking families, and to discuss the implications for the role of medical interpreters. METHODS: Using discourse analysis, we identified and categorized the various ways hospital-based interpreters adapted clinicians' language in 37 audio-recorded sessions in which Spanish-speaking parents participating in a clinical trial received their child's genomic sequencing results from English-speaking clinicians. RESULTS: We found that interpreters adapted clinicians' statements using five empathic linguistic tools: contextualization, encouragement, checking comprehension, endearment, and softening. Interpreters used an average of four linguistic tools per session, with contextualization and encouragement being the most frequently used. CONCLUSIONS: Interpreters used empathic linguistic tools to alter clinicians' statements when communicating genomic information to Spanish-speaking families. Our findings demonstrate the critical role of interpreters as cultural mediators and facilitators of understanding for Spanish-speaking families. PRACTICE IMPLICATIONS: This study expands upon the definition of clinical empathy in interpreter-mediated sessions. Our findings suggest that revisions of standards of medical interpretation practice may be warranted regarding interpreters' ability to adapt clinicians' language in a culturally sensitive manner during interpretation.


Subject(s)
Allied Health Personnel , Cultural Competency , Empathy , Genetic Counseling , Hispanic or Latino/psychology , Language , Multilingualism , Communication , Communication Barriers , Female , Genomics , Humans , Linguistics , Physician-Patient Relations , Translating
12.
J Genet Couns ; 2018 Aug 19.
Article in English | MEDLINE | ID: mdl-30121717

ABSTRACT

Genetic counseling is a rapidly expanding field, and the supply of certified genetic counselors is currently unable to keep up with job demand. Research is fairly limited regarding the awareness and perceptions that prospective genetic counseling students have on the field and what factors most influence their interest. The current study includes data collected from 1389 undergraduate students in the sciences at 23 universities across the United States who were surveyed regarding information related to their awareness, perceptions, knowledge, and interest in genetic counseling. The majority of participants had heard of genetic counseling (78.0%), many from a high school course (37.3%), college course (28.1%), or online (11.5%). Familiarity was associated with factors such as female gender (p = 0.003) and length of time in school (p < 0.001). After taking the survey, participant interest was positively associated with several factors including female gender (p < 0.001) and Asian and Hispanic ethnicity (p = 0.012). Factors commonly reported as attractive about the field included direct patient care, the variety of roles available, cultural competency and psychosocial training, and helping others. Discussion elaborates upon specific factors related to student awareness and interest in genetic counseling and potential ways to tailor recruitment strategies for maximum benefit to the field.

13.
Mol Genet Genomic Med ; 6(6): 898-909, 2018 11.
Article in English | MEDLINE | ID: mdl-30133189

ABSTRACT

BACKGROUND: Clinical genome and exome sequencing (CGES) is primarily used to address specific clinical concerns by detecting risk of future disease, clarifying diagnosis, or directing treatment. Additionally, CGES makes possible the disclosure of autosomal recessive and X-linked carrier results as additional secondary findings, and research about the impact of carrier results disclosure in this context is needed. METHODS: Representatives from 11 projects in the clinical sequencing exploratory research (CSER) consortium collected data from their projects using a structured survey. The survey focused on project characteristics, which variants were offered and/or disclosed to participants as carrier results, methods for carrier results disclosure, and project-specific outcomes. We recorded quantitative responses and report descriptive statistics with the aim of describing the variability in approaches to disclosing carrier results in translational genomics research projects. RESULTS: The proportion of participants with carrier results was related to the number of genes included, ranging from 3% (three genes) to 92% (4,600 genes). Between one and seven results were disclosed to those participants who received any positive result. Most projects offered participants choices about whether to receive some or all of the carrier results. There were a range of approaches to communicate results, and many projects used separate approaches for disclosing positive and negative results. CONCLUSION: Future translational genomics research projects will need to make decisions regarding whether and how to disclose carrier results. The CSER consortium experience identifies approaches that balance potential participant interest while limiting impact on project resources.


Subject(s)
Disclosure , Genetic Carrier Screening/methods , Genetic Counseling/methods , Facilities and Services Utilization , Genetic Carrier Screening/statistics & numerical data , Genetic Counseling/statistics & numerical data , Humans , Translational Research, Biomedical/methods , Whole Genome Sequencing/methods
14.
J Clin Invest ; 127(11): 4090-4103, 2017 Nov 01.
Article in English | MEDLINE | ID: mdl-28972538

ABSTRACT

Shwachman-Diamond syndrome (SDS) (OMIM #260400) is a rare inherited bone marrow failure syndrome (IBMFS) that is primarily characterized by neutropenia and exocrine pancreatic insufficiency. Seventy-five to ninety percent of patients have compound heterozygous loss-of-function mutations in the Shwachman-Bodian-Diamond syndrome (sbds) gene. Using trio whole-exome sequencing (WES) in an sbds-negative SDS family and candidate gene sequencing in additional SBDS-negative SDS cases or molecularly undiagnosed IBMFS cases, we identified 3 independent patients, each of whom carried a de novo missense variant in srp54 (encoding signal recognition particle 54 kDa). These 3 patients shared congenital neutropenia linked with various other SDS phenotypes. 3D protein modeling revealed that the 3 variants affect highly conserved amino acids within the GTPase domain of the protein that are critical for GTP and receptor binding. Indeed, we observed that the GTPase activity of the mutated proteins was impaired. The level of SRP54 mRNA in the bone marrow was 3.6-fold lower in patients with SRP54-mutations than in healthy controls. Profound reductions in neutrophil counts and chemotaxis as well as a diminished exocrine pancreas size in a SRP54-knockdown zebrafish model faithfully recapitulated the human phenotype. In conclusion, autosomal dominant mutations in SRP54, a key member of the cotranslation protein-targeting pathway, lead to syndromic neutropenia with a Shwachman-Diamond-like phenotype.


Subject(s)
Bone Marrow Diseases/genetics , Exocrine Pancreatic Insufficiency/genetics , Lipomatosis/genetics , Neutropenia/congenital , Signal Recognition Particle/genetics , Animals , Child , Congenital Bone Marrow Failure Syndromes , DNA Mutational Analysis , Female , Genetic Association Studies , Humans , Infant , Male , Models, Molecular , Neutropenia/genetics , Pancreas, Exocrine/metabolism , Phenotype , Protein Domains , Shwachman-Diamond Syndrome , Signal Recognition Particle/chemistry , Zebrafish
15.
Am J Hum Genet ; 101(4): 503-515, 2017 Oct 05.
Article in English | MEDLINE | ID: mdl-28942966

ABSTRACT

Bromodomain PHD finger transcription factor (BPTF) is the largest subunit of nucleosome remodeling factor (NURF), a member of the ISWI chromatin-remodeling complex. However, the clinical consequences of disruption of this complex remain largely uncharacterized. BPTF is required for anterior-posterior axis formation of the mouse embryo and was shown to promote posterior neuroectodermal fate by enhancing Smad2-activated wnt8 expression in zebrafish. Here, we report eight loss-of-function and two missense variants (eight de novo and two of unknown origin) in BPTF on 17q24.2. The BPTF variants were found in unrelated individuals aged between 2.1 and 13 years, who manifest variable degrees of developmental delay/intellectual disability (10/10), speech delay (10/10), postnatal microcephaly (7/9), and dysmorphic features (9/10). Using CRISPR-Cas9 genome editing of bptf in zebrafish to induce a loss of gene function, we observed a significant reduction in head size of F0 mutants compared to control larvae. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and phospho-histone H3 (PH3) staining to assess apoptosis and cell proliferation, respectively, showed a significant increase in cell death in F0 mutants compared to controls. Additionally, we observed a substantial increase of the ceratohyal angle of the craniofacial skeleton in bptf F0 mutants, indicating abnormal craniofacial patterning. Taken together, our data demonstrate the pathogenic role of BPTF haploinsufficiency in syndromic neurodevelopmental anomalies and extend the clinical spectrum of human disorders caused by ablation of chromatin remodeling complexes.


Subject(s)
Abnormalities, Multiple/genetics , Antigens, Nuclear/genetics , Craniofacial Abnormalities/genetics , Gene Expression Regulation, Developmental , Haploinsufficiency/genetics , Language Development Disorders/genetics , Microcephaly/genetics , Nerve Tissue Proteins/genetics , Transcription Factors/genetics , Abnormalities, Multiple/pathology , Adolescent , Animals , Antigens, Nuclear/metabolism , CRISPR-Cas Systems , Cell Proliferation , Cells, Cultured , Child , Child, Preschool , Chromatin Assembly and Disassembly , Cohort Studies , Craniofacial Abnormalities/pathology , Female , Gene Editing , Haploinsufficiency/physiology , Humans , Language Development Disorders/pathology , Larva/genetics , Larva/growth & development , Male , Microcephaly/pathology , Nerve Tissue Proteins/antagonists & inhibitors , Nerve Tissue Proteins/metabolism , Neurons/metabolism , Neurons/pathology , Phenotype , Transcription Factors/antagonists & inhibitors , Transcription Factors/metabolism , Zebrafish/genetics , Zebrafish/growth & development
16.
Per Med ; 14(6): 503-514, 2017 11.
Article in English | MEDLINE | ID: mdl-29749861

ABSTRACT

AIM: Describe modifications to technical genomic terminology made by interpreters during disclosure of whole exome sequencing (WES) results. PATIENTS & METHODS: Using discourse analysis, we identified and categorized interpretations of genomic terminology in 42 disclosure sessions where Spanish-speaking parents received their child's WES results either from a clinician using a medical interpreter, or directly from a bilingual physician. RESULTS: Overall, 76% of genomic terms were interpreted accordantly, 11% were misinterpreted and 13% were omitted. Misinterpretations made by interpreters and bilingual physicians included using literal and nonmedical terminology to interpret genomic concepts. CONCLUSION: Modifications to genomic terminology made during interpretation highlight the need to standardize bilingual genomic lexicons. We recommend Spanish terms that can be used to refer to genomic concepts.


Subject(s)
Exome Sequencing , Genetic Counseling/standards , Genomics , Professional-Family Relations , Terminology as Topic , Truth Disclosure , Child , Female , Genetic Counseling/methods , Hispanic or Latino , Humans , Male , Multilingualism , Neoplasms/genetics , Texas , Translating
17.
Cold Spring Harb Mol Case Stud ; 2(5): a001057, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27626068

ABSTRACT

The integration of genome-scale studies such as whole-exome sequencing (WES) into the clinical care of children with cancer has the potential to provide insight into the genetic basis of an individual's cancer with implications for clinical management. This report describes the results of clinical tumor and germline WES for a patient with a rare tumor diagnosis, rosette-forming glioneuronal tumor of the fourth ventricle (RGNT). Three pathogenic gene alterations with implications for clinical care were identified: somatic activating hotspot mutations in FGFR1 (p.N546K) and PIK3CA (p.H1047R) and a germline pathogenic variant in PTPN11 (p.N308S) diagnostic for Noonan syndrome. The molecular landscape of RGNT is not well-described, but these data are consistent with prior observations regarding the importance of the interconnected MAPK and PI3K/AKT/mTOR signaling pathways in this rare tumor. The co-occurrence of FGFR1, PIK3CA, and PTPN11 alterations provides further evidence for consideration of RGNT as a distinct molecular entity from pediatric low-grade gliomas and suggests potential therapeutic strategies for this patient in the event of tumor recurrence as novel agents targeting these pathways enter pediatric clinical trials. Although RGNT has not been definitively linked with cancer predisposition syndromes, two prior cases have been reported in patients with RASopathies (Noonan syndrome and neurofibromatosis type 1 [NF1]), providing an additional link between these tumors and the mitogen-activated protein kinase (MAPK) signaling pathway. In summary, this case provides an example of the potential for genome-scale sequencing technologies to provide insight into the biology of rare tumors and yield both tumor and germline results of potential relevance to patient care.

18.
Pediatr Blood Cancer ; 63(8): 1484-7, 2016 08.
Article in English | MEDLINE | ID: mdl-27100794

ABSTRACT

JAK2, MPL, and CALR mutations, which underlie essential thrombocythemia (ET) in most adults, are infrequent in children. Consequently, additional tests are needed to confirm pediatric ET diagnoses. We report a child with suspected ET and normal JAK2, MPL, and CALR analyses. Serum thrombopoietin (TPO) was markedly elevated, leading to analysis of the TPO gene, TPHO, which contains an upstream open reading frame (uORF) known to repress THPO translation. Sequencing revealed a de novo, germline stopgain mutation in the uORF, explaining the elevated TPO and thrombocytosis. This finding suggests that screening TPO levels and, if elevated, THPO 5' UTR sequencing could be diagnostic.


Subject(s)
Calreticulin/genetics , Janus Kinase 2/genetics , Receptors, Thrombopoietin/genetics , Thrombocythemia, Essential/diagnosis , Thrombocythemia, Essential/genetics , Thrombopoietin/blood , Humans , Infant , Male , Platelet Count , Thrombopoietin/genetics
19.
JAMA Oncol ; 2(5): 616-624, 2016 May 01.
Article in English | MEDLINE | ID: mdl-26822237

ABSTRACT

IMPORTANCE: Whole-exome sequencing (WES) has the potential to reveal tumor and germline mutations of clinical relevance, but the diagnostic yield for pediatric patients with solid tumors is unknown. OBJECTIVE: To characterize the diagnostic yield of combined tumor and germline WES for children with solid tumors. DESIGN: Unselected children with newly diagnosed and previously untreated central nervous system (CNS) and non-CNS solid tumors were prospectively enrolled in the BASIC3 study at a large academic children's hospital during a 23-month period from August 2012 through June 2014. Blood and tumor samples underwent WES in a certified clinical laboratory with genetic results categorized on the basis of perceived clinical relevance and entered in the electronic health record. MAIN OUTCOMES AND MEASURES: Clinical categorization of somatic mutations; frequencies of deleterious germline mutations related to patient phenotype and incidental medically-actionable mutations. RESULTS: Of the first 150 participants (80 boys and 70 girls, mean age, 7.4 years), tumor samples adequate for WES were available from 121 patients (81%). Somatic mutations of established clinical utility (category I) were reported in 4 (3%) of 121 patients, with mutations of potential utility (category II) detected in an additional 29 (24%) of 121 patients. CTNNB1 was the gene most frequently mutated, with recurrent mutations in KIT, TSC2, and MAPK pathway genes (BRAF, KRAS, and NRAS) also identified. Mutations in consensus cancer genes (category III) were found in an additional 24 (20%) of 121 tumors. Fewer than half of somatic mutations identified were in genes known to be recurrently mutated in the tumor type tested. Diagnostic germline findings related to patient phenotype were discovered in 15 (10%) of 150 cases: 13 pathogenic or likely pathogenic dominant mutations in adult and pediatric cancer susceptibility genes (including 2 each in TP53, VHL, and BRCA1), 1 recessive liver disorder with hepatocellular carcinoma (TJP2), and 1 renal diagnosis (CLCN5). Incidental findings were reported in 8 (5%) of 150 patients. Most patients harbored germline uncertain variants in cancer genes (98%), pharmacogenetic variants (89%), and recessive carrier mutations (85%). CONCLUSIONS AND RELEVANCE: Tumor and germline WES revealed mutations in a broad spectrum of genes previously implicated in both adult and pediatric cancers. Combined reporting of tumor and germline WES identified diagnostic and/or potentially actionable findings in nearly 40% of newly diagnosed pediatric patients with solid tumors.

20.
J Law Med Ethics ; 43(3): 529-37, 2015.
Article in English | MEDLINE | ID: mdl-26479562

ABSTRACT

The return of genetic research results after death in the pediatric setting comes with unique complexities. Researchers must determine which results and through which processes results are returned. This paper discusses the experience over 15 years in pediatric cancer genetics research of returning research results after the death of a child and proposes a preventive ethics approach to protocol development in order to improve the quality of return of results in pediatric genomic settings.


Subject(s)
Death , Disclosure/ethics , Genetic Research/ethics , Genomics/ethics , Neoplasms/genetics , Research Subjects , Adult , Child , Child, Preschool , Humans
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