Whole exome sequencing for non-selective pediatric patients with hyperlipidemia

Purpose To explore how parents of pediatric patients with cancer perceived the utility of clinical tumor and germline whole-exome sequencing (WES) results. Patients and Methods We conducted longitudinal interviews with parents of a diverse pediatric cancer population before disclosure of WES results (n = 64), then 1 to 8 months (n = 33) after disclosure. Interview transcripts were analyzed using a thematic qualitative approach. Results Parents identified a broad range of types of utility for their child’s WES results. Even when results did not affect their child’s current treatment, they expressed optimism about future clinical utility for their child, themselves, and other family members. Parents also reported experiencing psychological utility including peace of mind, relief of guilt, and satisfaction of curiosity. Pragmatic utility, such as the ability to plan for the future and make better reproductive decisions, was also described. Conclusion Parents of pediatric patients with cancer perceive WES to have broad utility, including psychological and pragmatic utility, even if there is no direct impact on clinical care. Additional research will need to consider how the value of genomic information should be characterized, how risks and benefits should be described, and how these results should inform recommendations and decisions about using WES.

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Whole-exome sequencing detects mutations in pediatric patients with atypical hemolytic uremic syndrome in Taiwan

Clinica Chimica Acta ◽

10.1016/j.cca.2019.03.1623 ◽

2019 ◽

Vol 494 ◽

pp. 143-150 ◽

Cited By ~ 2

Author(s):

Min-Hua Tseng ◽

Jeng-Daw Tsai ◽

I-Jung Tsai ◽

Shih-Ming Huang ◽

Jing-Long Huang ◽

...

Keyword(s):

Hemolytic Uremic Syndrome ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Pediatric Patients ◽

Atypical Hemolytic Uremic Syndrome ◽

Whole Exome ◽

Uremic Syndrome

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Exome Sequencing Identifies Recurring DNMT3A Mutations in Adult ETP-ALL

Blood ◽

10.1182/blood.v120.21.1377.1377 ◽

2012 ◽

Vol 120 (21) ◽

pp. 1377-1377

Author(s):

Martin Neumann ◽

Sandra Heesch ◽

Cornelia Schlee ◽

Stefan Schwartz ◽

Nicola Goekbuget ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Sanger Sequencing ◽

Somatic Mutations ◽

Pediatric Patients ◽

Genetic Alterations ◽

Whole Exome ◽

Repressor Complex ◽

Flt3 Mutations ◽

Exome Sequence

Abstract Abstract 1377 Introduction: Early T-cell precursor (ETP) ALL accounting for 10% of all T-ALL cases is of special interest because of its proposed origin from early thymic progenitors with multilineage differentiation potential. ETP-ALL is associated with a poorer outcome in pediatric and adult patients. On the molecular level, ETP-ALL is characterized by a specific immunophenotype (CD1-, CD5weak, CD8-, co-expression of stem cell and/or myeloid antigens) and distinct molecular features (expression of stem cell genes, high frequency of FLT3 mutations with absence of NOTCH1 mutations). Whereas a highly heterogeneous genetic pattern was revealed by whole genome sequencing in pediatric patients, the genetic background of adult ETP-ALL remains largely unknown. Here we investigated genetic alterations in adult ETP-ALL by whole exome sequencing and subsequently analyzed specific target genes. Patients and methods: We performed whole exome sequencing of five paired (diagnosis/remission) adult ETP-ALL patients enrolled in German Acute Lymphoblastic Leukemia Multicenter Study Group (GMALL) trials. Using exon capturing from genomic DNA, followed by 76-bp paired-end sequencing on an Illumina Genome Analyzer IIx platform, we generated at least 5 Gb of exome sequence from each ETP-ALL and remission samples. Somatic mutations were identified by comparing the ETP-ALL with the remission exome sequence, excluding all annotated polymorphisms (dbSNP130), non-coding positions and positions with evidence of a variant in the corresponding remission samples. Candidate variants were confirmed by capillary sequencing of genomic DNA. The DNMT3A mutations status was analyzed by Sanger sequencing of exons 11–23 in additional 68 adult ETP-ALL (55 male, 13 female, median age: 38 years) as well as the mutation status of the polycomb repressor complex (PRC) genes EZH2 and SUZ12. For 52 of 68 patients clinical follow-up data were available. Results: Using whole exome sequencing we found a total of 56 non-synonymous somatic mutations or indels in the five ETP-ALL patients (range: 6 to 16 per patient). Eleven mutations/indels affected cancer genes. DNMT3A (2/5) and FAT3 (2/5) were recurrently mutated in the five patients. The DNA-methyl-transferase DNMT3A is a frequent mutational target in acute myeloid leukemia (AML; 20%), whereas FAT3 (FAT, tumor suppressor homolog 3) mutations were recently reported in ovarian carcinoma (TCGA, Nature 2011). Novel mutations identified in adult ETP-ALL involved genes in epigenetic regulation (e.g. MLL2, MLL3, BMI1), and in genes previously reported to be mutated in ETP-ALL (e.g. in JAK1, ETV6, NOTCH1, DNM2). By Sanger sequencing, we screened for DNMT3A mutations in a larger cohort of adult ETP-ALL. DNMT3A mutations were present in 11 of the 68 (16%) patients, a mutation rate similar to AML. Amino acid R882 (exon 23), the most frequently mutated amino acid in AML, was mutated in five ETP-ALL. The remaining six mutations occurred in single spots, with one exception in the ZNF or the MTF domain. Patients with a DNMT3A mutation were significantly older (median: 63 vs 37 years, P=0.016). No correlation was found between DNMT3A and FLT3 mutations (27% in DNMT3A mut pts. vs. 37% in DNMT3A wt pts., P=0.41) or NOTCH1 mutations (10% in DNMT3A mut pts. vs. 16% in DNMT3A wt pts., P=0.47). In addition, we investigated genetic alterations in epigenetic regulators including members of the polycomb repressor complex (PRC). Mutations were seen in EZH2 in 4/68 (6%), SUZ12 in 1/68 (1%) and SH2B3 in 4/69 (6%) of ETP-ALL. Interestingly, patients with at least one mutation in an epigenetic regulator gene (DNMT3A, SUZ12, SH2B3, MLL2, or EZH2) showed a trend towards an inferior survival (one-year-survival: 50% vs. 85%, P=0.08). Conclusion: Adult ETP-ALL patients display a heterogenous spectrum of mutations, particularly affecting genes involved in epigenetic regulation. The spectrum is different to pediatric patients with a lower rate of polycomb repressor complex and a higher rate of DNMT3A mutations. The higher rate of DNMT3A mutations in older patients might point to a different pathogenesis compared to pediatric ETP-ALL. Like in AML, DNMT3A mutations in adult ETP-ALL show a similar frequency, within the same hot spots and are correlated with an adverse prognostic value, underscoring the myeloid character of ETP-ALL. Thus, these data may provide a rationale to use epigenetic therapy in ETP-ALL. Disclosures: Krebs: Illumina: Honoraria. Greif:Illumina: Honoraria.

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Comprehensive genetic analysis by whole exome sequencing in 352 Korean pediatric patients with unknown neurodevelopmental disorders

10.1101/472803 ◽

2018 ◽

Author(s):

Youngha Lee ◽

Jin Sook Lee ◽

Soo Yeon Kim ◽

Jaeso Cho ◽

Yongjin Yoo ◽

...

Keyword(s):

Genetic Analysis ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Genetic Variants ◽

Neurodevelopmental Disorders ◽

Pediatric Patients ◽

Medical System ◽

Pathogenic Variants ◽

Whole Exome ◽

Novel Variants

AbstractImportanceAccurate diagnosis of pediatric patients with complicated neurological problems demands a well-coordinated combination of robust genetic analytic capability and delicate clinical evaluation. It should be tested whether this challenge can be augmented by whole exome sequencing (WES).ObjectiveTo evaluate the utility of WES-based diagnosis and discovery of novel variants of undiagnosed patients with complex neurodevelopmental problems in a country with a centralized medical system.Design, setting, and participantsA cohort of 352 Korean patients, believed to cover a major portion of the entire country from July 2014 to April 2017, with a broad spectrum of neurodevelopmental disorders without any pathogenic variants revealed by conventional methods were evaluated by trio-based WES at Seoul National University Children’s Hospital.ExposuresWES of patients and parents and subsequent evaluation of genetic variants.Main outcomes and measuresGenetic variants from each patient were evaluated for known disease association and novel variants were assessed for possible involvement with neurodevelopment process.ResultsWe identified disease-causing variants, including newly discovered variants, in 57.4% of the probands, who had underwent a mean of 5.6 years of undiagnosed periods and visited mean of 2.3 tertiary hospitals. The cohort included 112 patients with variants that were previously reported as pathogenic (31.8%), 16 patients with copy number variants (4.5%) and 27 patients with variants that were associated with different clinical symptoms (7.7%). We also discovered potentially pathogenic variants from 47 patients that required further functional assessments (13.4%) and demonstrated potential implications in neurodevelopmental disorders. Following the genetic analysis, we provided more precise treatments to selected patients. A few clinical vignettes are presented that illuminate the potential diagnostic pitfalls that one could have encountered without this approach.Conclusions and relevanceOur results highlight the utility of WES-based diagnosis for improved patient care in a country with a centralized medical system and discovery of novel pathophysiology mechanisms.Key pointsQuestionWhat is the advantage of whole exome sequencing based diagnosis of pediatric neurology patients with unknown rare symptoms in a large tertiary clinic in a country with a centralized medical system?FindingsWhole exome sequencing of 352 Korean patients, with a mean of 5.7 years of undiagnosed period, yielded 44.0% of conservative diagnostic yield. A number of cases were directly benefitted by trio-based WES via termination of diagnostic odyssey, genetic counseling for next offspring, or suggestion of more effective and customized treatment options.MeaningWe report on the establishment of a national-level whole exome-based diagnosis system, with emphasis on deliberate integration of clinical interpretation and genetic analysis. Whole exome sequencing should be a choice of diagnostic tools for pediatric neurologic patients with ambiguous symptoms.

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GENE-30. PRELIMINARY STUDY ON WHOLE-EXOME SEQUENCING TECHNOLOGY IN THE GENETIC ANALYSIS OF PEDIATRIC PATIENTS WITH GLIOMAS

Neuro-Oncology ◽

10.1093/neuonc/noz175.432 ◽

2019 ◽

Vol 21 (Supplement_6) ◽

pp. vi104-vi104

Author(s):

Mingyao Lai ◽

Juan Li ◽

Junjie Zhen ◽

jiangfen zhou ◽

Qingjun Hu ◽

...

Keyword(s):

Genetic Analysis ◽

Signaling Pathways ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Pediatric Patients ◽

Genetic Mutation ◽

Pleomorphic Xanthoastrocytoma ◽

Pathological Examination ◽

Sequencing Technology ◽

Whole Exome

Abstract OBJECTIVE To analyze the genes related to the signaling pathways in pediatric gliomas and drug-related genes with whole-exome sequencing technology. METHODS The tumor tissues and matched blood samples of 17 enrolled patients were detected with whole-exome sequencing technology. There were 3 cases of diffuse midline gliomas, 2 cases of childhood glioblastomas, 3 cases of disffuse astrocytoma, 1 case of pleomorphic xanthoastrocytoma, 1 case of ganglioglioma, 6 cases of anaplastic ependymoma and 1 case of ependymoma in this study. All the enrolled patients who were no more than 14 years old received surgery in the Department of Neurosurgery, Guangdong Sanjiu Brain Hospital. The diagnosis was confirmed by pathological examination and the sample acquisition was approved by hospital ethics committee. RESULTS With the use of whole-exome sequencing technology, a total of 31 related genetic mutations were detected in 15 cases, while no genetic mutation was detected in the other 2 cases. The genes related to the signaling pathways in pediatric gliomas included ATRX, ASL1, BCOR, EP300, FGFR1, H3F3A, IGF1R, MED12, PIK3R1, PRKDC, RB1, SETD2, SMARCA4, SOX2, TGFBR2, and the drug-related genes included AKT1, BCL2, BRAF, BRCA2, CCND1, CCND2, CDK6, EGFR, FGF3, KRAS, MET, PDGFRA, PIK3CA, PTEN, TP53, TSC1. One patient only had genes related to the signaling pathways, and 14 patients had drug-related genes. CONCLUSION Applying whole-exome sequencing technology in the genetic analysis of pediatric patients with gliomas has remarkable guiding significance for revealing the mechanism of disease, searching for therapeutic targets and adopting individualized treatment, which can bring potential benefits to pediatric patients. However, more samples and further data analysis and verification are needed in future study.

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Is Whole-Exome Sequencing an Ethically Disruptive Technology? Perspectives of Pediatric Oncologists and Parents of Pediatric Patients With Solid Tumors

Pediatric Blood & Cancer ◽

10.1002/pbc.25815 ◽

2015 ◽

Vol 63 (3) ◽

pp. 511-515 ◽

Cited By ~ 25

Author(s):

Laurence B. McCullough ◽

Melody J. Slashinski ◽

Amy L. McGuire ◽

Richard L. Street ◽

Christine M. Eng ◽

...

Keyword(s):

Exome Sequencing ◽

Solid Tumors ◽

Whole Exome Sequencing ◽

Pediatric Patients ◽

Disruptive Technology ◽

Whole Exome

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Application of Trio-Whole Exome Sequencing in Genetic Diagnosis and Therapy in Chinese Children With Epilepsy

Frontiers in Molecular Neuroscience ◽

10.3389/fnmol.2021.699574 ◽

2021 ◽

Vol 14 ◽

Author(s):

Tiejia Jiang ◽

Jia Gao ◽

Lihua Jiang ◽

Lu Xu ◽

Congying Zhao ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Copy Number ◽

Pediatric Patients ◽

De Novo ◽

Treatment Options ◽

Copy Number Variants ◽

Genetic Diagnosis ◽

Single Nucleotide Variants ◽

Whole Exome

Epilepsy is one of the most common neurological disorders in pediatric patients with other underlying neurological defects. Identifying the underlying etiology is crucial for better management of the disorder. We performed trio-whole exome sequencing in 221 pediatric patients with epilepsy. Probands were divided into seizures with developmental delay/intellectual disability (DD/ID) and seizures without DD/ID groups. Pathogenic (P) or likely pathogenic (LP) variants were identified in 71/110 (64.5%) patients in the seizures with DD/ID group and 21/111 (18.9%) patients in the seizures without DD/ID group (P < 0.001). Eighty-seven distinct P/LP single nucleotide variants (SNVs)/insertion deletions (Indels) were detected, with 55.2% (48/87) of them being novel. All aneuploidy and P/LP copy number variants (CNVs) larger than 100 Kb were identifiable by both whole-exome sequencing and copy number variation sequencing (CNVseq) in 123 of individuals (41 pedigrees). Ten of P/LP CNVs in nine patients and one aneuploidy variant in one patient (Patient #56, #47, XXY) were identified by CNVseq. Herein, we identified seven genes (NCL, SEPHS2, PA2G4, SLC35G2, MYO1C, GPR158, and POU3F1) with de novo variants but unknown pathogenicity that were not previously associated with epilepsy. Potential effective treatment options were available for 32 patients with a P/LP variant, based on the molecular diagnosis. Genetic testing may help identify the molecular etiology of early onset epilepsy and DD/ID and further aid to choose the appropriate treatment strategy for patients.

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Analysis of WT1 Mutations and Combined Aberrations in Childhood Acute Myeloid Leukemia using Whole Exome Sequencing

Blood ◽

10.1182/blood.v124.21.2340.2340 ◽

2014 ◽

Vol 124 (21) ◽

pp. 2340-2340

Author(s):

Nils von Neuhoff ◽

Peter Husemann ◽

Robert Geffers ◽

Christiane Walter ◽

Christine von Neuhoff ◽

...

Keyword(s):

Dna Sequencing ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Pediatric Patients ◽

Conflicts Of Interest ◽

Average Length ◽

Genetic Profile ◽

Ras Gene ◽

Whole Exome ◽

Sequencing Library

Abstract Introduction: Mutations in the WT1 zinc finger gene (OMIM: 607102) are associated with an unfavorable clinical outcome in pediatric AML (Ho et al. 2010). In a subgroup of WT1mut patients additional mutations in other AML typical genes like FLT3 are also detectable. Balgobind et al. (2011) showed a worst outcome for pediatric patients with WT1-mutations combined with a FLT3-ITD (5-year overall survival=0,22, SE= 0,14). We and others identified combined mutations not only in the FLT3-TKD but also other genes like NPM1, nRAS or c-KIT. Using DNA from WT1mut AML pediatric patients with combined mutations, we performed whole exome sequencing (WES) to identify additional genetic aberrations to gain further insight into the genetic profile of this disease. Methods: From a cohort of 19 WT1mut patients, we selected 10 patients with CN and additional mutations in the FLT3-TKD, NPM1 or n-RAS gene. Concentration and quality of the purified genomic DNA (gDNA) was determined by Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). Fragmentation of 100ng gDNA was performed on a Covaris S2 (duty cycle 10%, intensity 4, 200 cycles per burst for 80s) to obtain fragments with an average length of 300 base pairs (bp). The DNA sequencing library was generated from 100ng of fragmented gDNA using Agilent SureSelectXT Reagent Kits v5 (50Mb) according to the manufacturer´s protocols. The final DNA sequencing library was purified, size-controlled by Agilent Technologies 2100 Bioanalyzer (High Sensitivity DNA Chip) and prepared for sequencing according to the manufacturer´s protocol (Illumina). The libraries were sequenced on Illumina HiSeq2500 using TruSeq SBS Kit v3-HS (200 cycles, paired end run) with an average of 12.5 x 106 reads per single exome (mean coverage: 50x). The GATK Pipeline (GenomeAnalysisTK-1.7) was applied for read quality trimming, read alignment to reference (hg19) and quality trimmed variant calling (McKenna et al., 2010). Variant annotation was done using Annovar (Wang et al., 2010). Results: In 19 out of 164 patients, who were screened for WT1, mutations in exon 7 or 9 of the WT1- gene were detected. Patients with WT1mut had an inferior 2-years event free survival compared to patients with WTwt (0.18, SE=0.09 vs. 0.61, SE=0.04, p=0,0001). DNA from WT1mut patients (n=10) with normal karyotype CN and additional mutations in the FLT3-TKD, NPM1- , or the n-RAS gene were elected for WES. The Annovar annotation suggests that each sample contains 5,359 – 5,480 genes that are mutated and where the mutations are predicted to have an effect. 2,324 of these mutated genes were present in all 10 samples together. After review of the literature, ZNF717, MUC16, MAP2K3, PRIM2, PKD1L2, MUC6, CDC27, TTN and MUC5B were identified as candidates for ongoing validation analysis. With respect to functional correlation, 90 - 113 frameshift deletions, 68 - 93 frameshift insertions, 103 - 125 non-frameshift deletions, and 96 - 118 non-frameshift insertions were predicted. Discussion: WT1mut AML pediatric patients with combined mutations in other AML- specific genes present a special subgroup with an adverse prognosis. Nevertheless, more information about the genetic network is necessary to understand the pathobiology and to improve treatment of the disease. For this purpose, we decided to perform whole exome sequencing in 10 samples from patients who were treated after the AML BFM 04 protocol. We identified mutations in more than 9 genes and several aberrations in functional regions of all samples. Currently, validation of these findings is being performed to evaluate the role of the mutated genes. Nevertheless, the results of this analysis will also shed also light onto the clonal evolution of the leukemic clone and the importance for the treatment and the prognosis of the patients. Disclosures No relevant conflicts of interest to declare.

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