DICER1 Mutations in the Era of Expanding Integrative Clinical Sequencing in Pediatric Oncology

PURPOSE DICER1 syndrome is a recently described inherited cancer predisposition syndrome caused by pathogenic variants in DICER1. With the recent increase in integrative clinical sequencing for pediatric patients with cancer, our understanding of the DICER1 syndrome continues to evolve, as new and rare pathogenic variants are reported. As the frequency of integrative clinical sequencing increases, discussions regarding challenges encountered in the interpretation of sequencing results are essential to continue to advance the field of cancer predisposition. The purpose of this work was to identify patients with somatic and/or germline DICER1 variants in our patient population and to discuss sequencing interpretation and the clinical recommendations that result from the integrative clinical sequencing results. METHODS Patients were enrolled in the PEDS-MIONCOSEQ study. This integrative clinical sequencing study includes paired tumor/normal whole-exome sequencing and tumor transcriptome sequencing. Patients identified as having DICER1 variants were included. RESULTS We report a DICER1 variant of unknown clinical significance in a patient with a highly unusual response to therapy. Two patients had diagnoses clarified once the integrative clinical sequencing revealing a DICER1 variant was available. We also discovered a patient with low-level DICER1 mosaicism and the challenges encountered in the sequencing interpretation for this patient. In addition to the sequencing data and result interpretation, this work also highlights testing and screening recommendations made to patients with DICER1 variants and their families on the basis of these results. CONCLUSION This work serves to extend the DICER1 phenotype and advance the utility of clinical integrative sequencing in the fields of pediatric oncology and cancer genetic predisposition.

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Using family history forms in pediatric oncology to identify patients for genetic assessment

Current Oncology ◽

10.3747/co.24.3710 ◽

2017 ◽

Vol 24 (6) ◽

pp. 441 ◽

Cited By ~ 2

Author(s):

A. Hamilton ◽

E. Smith ◽

J. Hamon ◽

E. Tomiak ◽

M. Bassal ◽

...

Keyword(s):

Genetic Testing ◽

Family History ◽

Pediatric Oncology ◽

Small Sample ◽

Cancer Predisposition ◽

Candidate Gene Approach ◽

Inherited Cancer ◽

Cancer Predisposition Syndrome ◽

Pediatric Cancer Patients ◽

History Of

Objective We set out to identify and offer genetic testing to the 5%–10% of pediatric cancer patients who have been estimated to carry germline mutations in inherited cancer predisposition syndromes. Clinical genetic testing has become widely available, and thus in busy oncology clinics, tools are needed to identify patients who could benefit from a referral to genetics.Methods We studied the clinical utility of administering a family history form in the pediatric oncology long-term follow-up clinic to identify patients who might have an inherited cancer predisposition syndrome. Genetic testing involved primarily Sanger sequencing in clia (Clinical Laboratory Improvement Amendments)–certified laboratories.Results Of 57 patients who completed forms, 19 (33.3%) met criteria for referral to genetics. A significant family history of cancer was present for 4 patients, and 12 patients underwent genetic testing. Of 18 genetic tests ordered, none identified a pathogenic mutation, likely because of a small sample size and a candidate-gene approach to testing. Three families were also identified for further assessment based on a family history of breast cancer, with two of families having members eligible for BRCA1 and BRCA2 testing.Conclusions Genetic testing in pediatric oncology patients is important to guide the management of patients who have an inherited cancer predisposition syndrome and to identify other family members at risk when mutations are identified. When no mutations are identified, that information is often reassuring to families who are worried about siblings. However, in the absence of an identified genetic cause in a patient, some uncertainty remains.

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The ICR639 CPG NGS validation series: A resource to assess analytical sensitivity of cancer predisposition gene testing

Wellcome Open Research ◽

10.12688/wellcomeopenres.14594.1 ◽

2018 ◽

Vol 3 ◽

pp. 68

Author(s):

Shazia Mahamdallie ◽

Elise Ruark ◽

Esty Holt ◽

Emma Poyastro-Pearson ◽

Anthony Renwick ◽

...

Keyword(s):

Copy Number Variations ◽

Cancer Predisposition ◽

Validation Dataset ◽

Small Scale ◽

Real Sequence ◽

Analytical Sensitivity ◽

Sequencing Data ◽

Pathogenic Variants ◽

Gene Testing ◽

Validation Series

The analytical sensitivity of a next generation sequencing (NGS) test reflects the ability of the test to detect real sequence variation. The evaluation of analytical sensitivity relies on the availability of gold-standard, validated, benchmarking datasets. For NGS analysis the availability of suitable datasets has been limited. Most laboratories undertake small scale evaluations using in-house data, and/or rely on in silico generated datasets to evaluate the performance of NGS variant detection pipelines. Cancer predisposition genes (CPGs), such as BRCA1 and BRCA2, are amongst the most widely tested genes in clinical practice today. Hundreds of providers across the world are now offering CPG testing using NGS methods. Validating and comparing the analytical sensitivity of CPG tests has proved difficult, due to the absence of comprehensive, orthogonally validated, benchmarking datasets of CPG pathogenic variants. To address this we present the ICR639 CPG NGS validation series. This dataset comprises data from 639 individuals. Each individual has sequencing data generated using the TruSight Cancer Panel (TSCP), a targeted NGS assay for the analysis of CPGs, together with orthogonally generated data showing the presence of at least one CPG pathogenic variant per individual. The set consists of 645 pathogenic variants in total. There is strong representation of the most challenging types of variants to detect, with 339 indels, including 16 complex indels and 24 with length greater than five base pairs and 74 exon copy number variations (CNVs) including 23 single exon CNVs. The series includes pathogenic variants in 31 CPGs, including 502 pathogenic variants in BRCA1 or BRCA2, making this an important comprehensive validation dataset for providers of BRCA1 and BRCA2 NGS testing. We have deposited the TSCP FASTQ files of the ICR639 series in the European Genome-phenome Archive (EGA) under accession number EGAD00001004134.

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Germline cancer predisposition variants and pediatric glioma: a population-based study in California

Neuro-Oncology ◽

10.1093/neuonc/noaa014 ◽

2020 ◽

Vol 22 (6) ◽

pp. 864-874 ◽

Cited By ~ 4

Author(s):

Ivo S Muskens ◽

Adam J de Smith ◽

Chenan Zhang ◽

Helen M Hansen ◽

Libby Morimoto ◽

...

Keyword(s):

Cell Cycle Control ◽

Population Level ◽

Cancer Predisposition ◽

Sequencing Data ◽

Pediatric Glioma ◽

Germline Variants ◽

Pathogenic Variants ◽

Predisposition Genes ◽

Pediatric Astrocytoma ◽

Pediatric Glioblastoma

Abstract Background Pediatric astrocytoma constitutes a majority of malignant pediatric brain tumors. Previous studies that investigated pediatric cancer predisposition have primarily been conducted in tertiary referral centers and focused on cancer predisposition genes. In this study, we investigated the contribution of rare germline variants to risk of malignant pediatric astrocytoma on a population level. Methods DNA samples were extracted from neonatal dried bloodspots from 280 pediatric astrocytoma patients (predominantly high grade) born and diagnosed in California and were subjected to whole-exome sequencing. Sequencing data were analyzed using agnostic exome-wide gene-burden testing and variant identification for putatively pathogenic variants in 175 a priori candidate cancer-predisposition genes. Results We identified 33 putatively pathogenic germline variants among 31 patients (11.1%) which were located in 24 genes largely involved in DNA repair and cell cycle control. Patients with pediatric glioblastoma were most likely to harbor putatively pathogenic germline variants (14.3%, N = 9/63). Five variants were located in tumor protein 53 (TP53), of which 4 were identified among patients with glioblastoma (6.3%, N = 4/63). The next most frequently mutated gene was neurofibromatosis 1 (NF1), in which putatively pathogenic variants were identified in 4 patients with astrocytoma not otherwise specified. Gene-burden testing also revealed that putatively pathogenic variants in TP53 were significantly associated with pediatric glioblastoma on an exome-wide level (odds ratio, 32.8, P = 8.04 × 10−7). Conclusion A considerable fraction of pediatric glioma patients, especially those of higher grade, harbor a putatively pathogenic variant in a cancer predisposition gene. Some of these variants may be clinically actionable or may warrant genetic counseling.

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Whole-Exome Sequencing and C9orf72 Analysis in Primary Progressive Aphasia

Journal of Alzheimer s Disease ◽

10.3233/jad-201310 ◽

2021 ◽

pp. 1-6

Author(s):

Vanesa Pytel ◽

Laura Hernández-Lorenzo ◽

Laura Torre-Fuentes ◽

Raúl Sanz ◽

Nieves González ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Primary Progressive Aphasia ◽

Sequencing Data ◽

Progressive Aphasia ◽

Primary Progressive ◽

Pathogenic Variants ◽

Whole Exome ◽

Whole Exome Sequencing Data ◽

Sporadic Disease

Primary progressive aphasia (PPA) is mainly considered a sporadic disease and few studies have systematically analyzed its genetic basis. We here report the analyses of C9orf72 genotyping and whole-exome sequencing data in a consecutive and well-characterized cohort of 50 patients with PPA. We identified three pathogenic GRN variants, one of them unreported, and two cases with C9orf72 expansions. In addition, one likely pathogenic variant was found in the SQSTM1 gene. Overall, we found 12%of patients carrying pathogenic or likely pathogenic variants. These results support the genetic role in the pathophysiology of a proportion of patients with PPA.

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Comprehensive germline-genomic and clinical profiling in 160 unselected children and adolescents with cancer

European Journal of Human Genetics ◽

10.1038/s41431-021-00878-x ◽

2021 ◽

Author(s):

Rabea Wagener ◽

Julia Taeubner ◽

Carolin Walter ◽

Layal Yasin ◽

Deya Alzoubi ◽

...

Keyword(s):

Target Genes ◽

Strong Association ◽

Clinical Work ◽

Cancer Predisposition ◽

Structural Variants ◽

Cancer Predisposition Syndrome ◽

Whole Exome ◽

Single Center Study ◽

Genetic Mechanisms ◽

Work Up

AbstractIn childhood cancer, the frequency of cancer-associated germline variants and their inheritance patterns are not thoroughly investigated. Moreover, the identification of children carrying a genetic predisposition by clinical means remains challenging. In this single-center study, we performed trio whole-exome sequencing and comprehensive clinical evaluation of a prospectively enrolled cohort of 160 children with cancer and their parents. We identified in 11/160 patients a pathogenic germline variant predisposing to cancer and a further eleven patients carried a prioritized VUS with a strong association to the cancerogenesis of the patient. Through clinical screening, 51 patients (31.3%) were identified as suspicious for an underlying cancer predisposition syndrome (CPS), but only in ten of those patients a pathogenic variant could be identified. In contrast, one patient with a classical CPS and ten patients with prioritized VUS were classified as unremarkable in the clinical work-up. Taken together, a monogenetic causative variant was detected in 13.8% of our patients using WES. Nevertheless, the still unclarified clinical suspicious cases emphasize the need to consider other genetic mechanisms including new target genes, structural variants, or polygenic interactions not previously associated with cancer predisposition.

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ZNF445: a homozygous truncating variant in a patient with Temple syndrome and multilocus imprinting disturbance

Clinical Epigenetics ◽

10.1186/s13148-021-01106-5 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Masayo Kagami ◽

Kaori Hara-Isono ◽

Keiko Matsubara ◽

Kazuhiko Nakabayashi ◽

Satoshi Narumi ◽

...

Keyword(s):

Methylation Pattern ◽

Aberrant Methylation ◽

Sequencing Analysis ◽

Sequencing Data ◽

Clinically Normal ◽

Pathogenic Variants ◽

Whole Exome ◽

Whole Exome Sequencing Data ◽

Temple Syndrome ◽

First Time

Abstract Background ZNF445, as well as ZFP57, is involved in the postfertilization methylation maintenance of multiple imprinting-associated differentially methylated regions (iDMRs). Thus, ZNF445 pathogenic variants are predicted to cause multilocus imprinting disturbances (MLIDs), as do ZFP57 pathogenic variants. In particular, the MEG3/DLK1:IG-DMR would be affected, because the postzygotic methylation imprint of the MEG3/DLK1:IG-DMR is maintained primarily by ZNF445, whereas that of most iDMRs is preserved by both ZFP57 and ZNF445 or primarily by ZFP57. Results We searched for a ZNF445 variant(s) in six patients with various imprinting disorders (IDs) caused by epimutations and MLIDs revealed by pyrosequencing for nine iDMRs, without a selection for the original IDs. Re-analysis of the previously obtained whole exome sequencing data identified a homozygous ZNF445 variant (NM_181489.6:c.2803C>T:p.(Gln935*)) producing a truncated protein missing two of 14 zinc finger domains in a patient with Temple syndrome and MLID. In this patient, array-based genomewide methylation analysis revealed severe hypomethylation of most CpGs at the MEG3:TSS-DMR, moderate hypomethylation of roughly two-thirds of CpGs at the H19/IGF2:IG-DMR, and mild-to-moderate hypomethylation of a few CpGs at the DIRAS3:TSS-DMR, MEST:alt-TSS-DMR, IGF2:Ex9-DMR, IGF2:alt-TSS, and GNAS-AS1:TSS-DMR. Furthermore, bisulfite sequencing analysis for the MEG3/DLK1:IG-DMR delineated a markedly hypomethylated segment (CG-A). The heterozygous parents were clinically normal and had virtually no aberrant methylation pattern. Conclusions We identified a ZNF445 pathogenic variant for the first time. Since ZNF445 binds to the MEG3/DLK1:IG-DMR and other iDMRs affected in this patient, the development of Temple syndrome and MLID would primarily be explained by the ZNF445 variant. Furthermore, CG-A may be the target site for ZNF445 within the MEG3/DLK1:IG-DMR.

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Mutations in genes encoding regulators of mRNA decapping and translation initiation: links to intellectual disability

Biochemical Society Transactions ◽

10.1042/bst20200109 ◽

2020 ◽

Vol 48 (3) ◽

pp. 1199-1211 ◽

Cited By ~ 2

Author(s):

Dominique Weil ◽

Amélie Piton ◽

Davor Lessel ◽

Nancy Standart

Keyword(s):

Intellectual Disability ◽

Rna Binding ◽

Rna Binding Proteins ◽

Sequencing Data ◽

Rna Helicases ◽

Mrna Decapping ◽

Pathogenic Variants ◽

Whole Exome ◽

Genes Encoding ◽

Post Transcriptional Regulation

Intellectual disability (ID) affects at least 1% of the population, and typically presents in the first few years of life. ID is characterized by impairments in cognition and adaptive behavior and is often accompanied by further delays in language and motor skills, as seen in many neurodevelopmental disorders (NDD). Recent widespread high-throughput approaches that utilize whole-exome sequencing or whole-genome sequencing have allowed for a considerable increase in the identification of these pathogenic variants in monogenic forms of ID. Notwithstanding this progress, the molecular and cellular consequences of the identified mutations remain mostly unknown. This is particularly important as the associated protein dysfunctions are the prerequisite to the identification of targets for novel drugs of these rare disorders. Recent Next-Generation sequencing-based studies have further established that mutations in genes encoding proteins involved in RNA metabolism are a major cause of NDD. Here, we review recent studies linking germline mutations in genes encoding factors mediating mRNA decay and regulators of translation, namely DCPS, EDC3, DDX6 helicase and ID. These RNA-binding proteins have well-established roles in mRNA decapping and/or translational repression, and the mutations abrogate their ability to remove 5′ caps from mRNA, diminish their interactions with cofactors and stabilize sub-sets of transcripts. Additional genes encoding RNA helicases with roles in translation including DDX3X and DHX30 have also been linked to NDD. Given the speed in the acquisition, analysis and sharing of sequencing data, and the importance of post-transcriptional regulation for brain development, we anticipate mutations in more such factors being identified and functionally characterized.

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Whole-exome sequencing of a large Chinese azoospermia and severe oligospermia cohort identifies novel infertility causative variants and genes

Human Molecular Genetics ◽

10.1093/hmg/ddaa101 ◽

2020 ◽

Vol 29 (14) ◽

pp. 2451-2459

Author(s):

Shitao Chen ◽

Guishuan Wang ◽

Xiaoguo Zheng ◽

Shunna Ge ◽

Yubing Dai ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Molecular Characteristics ◽

Obstructive Azoospermia ◽

Sequencing Data ◽

Chinese Han ◽

Functional Studies ◽

Variants Of Unknown Significance ◽

Pathogenic Variants ◽

Whole Exome

Abstract Rare coding variants have been proven to be one of the significant factors contributing to spermatogenic failure in patients with non-obstructive azoospermia (NOA) and severe oligospermia (SO). To delineate the molecular characteristics of idiopathic NOA and SO, we performed whole-exome sequencing of 314 unrelated patients of Chinese Han origin and verified our findings by comparing to 400 fertile controls. We detected six pathogenic/likely pathogenic variants and four variants of unknown significance, in genes known to cause NOA/SO, and 9 of which had not been earlier reported. Additionally, we identified 20 novel NOA candidate genes affecting 25 patients. Among them, five (BRDT, CHD5, MCM9, MLH3 and ZFX) were considered as strong candidates based on the evidence obtained from murine functional studies and human single-cell (sc)RNA-sequencing data. These genetic findings provide insight into the aetiology of human NOA/SO and pave the way for further functional analysis and molecular diagnosis of male infertility.

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Comprehensive Exonic Sequencing of Hemiplegic Migraine-Related Genes in a Cohort of Suspected Probands Identifies Known and Potential Pathogenic Variants

Cells ◽

10.3390/cells9112368 ◽

2020 ◽

Vol 9 (11) ◽

pp. 2368

Author(s):

Heidi G. Sutherland ◽

Neven Maksemous ◽

Cassie L. Albury ◽

Omar Ibrahim ◽

Robert A. Smith ◽

...

Keyword(s):

Genetic Testing ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Genetic Factors ◽

Sequencing Data ◽

Hemiplegic Migraine ◽

Pathogenic Variants ◽

Targeted Analysis ◽

Whole Exome ◽

Whole Exome Sequencing Data

Hemiplegic migraine (HM) is a rare migraine disorder with aura subtype including temporary weakness and visual, sensory, and/or speech symptoms. To date, three main genes—CACNA1A, ATP1A2, and SCN1A—have been found to cause HM. These encode ion channels or transporters, important for regulating neuronal ion balance and synaptic transmission, leading to HM being described as a channelopathy. However, <20% of HM cases referred for genetic testing have mutations in these genes and other genes with roles in ion and solute transport, and neurotransmission has also been implicated in some HM cases. In this study, we performed whole exome sequencing for 187 suspected HM probands referred for genetic testing, but found to be negative for CACNA1A, ATP1A2, and SCN1A mutations, and applied targeted analysis of whole exome sequencing data for rare missense or potential protein-altering variants in the PRRT2, PNKD, SLC1A3, SLC2A1, SLC4A4, ATP1A3, and ATP1A4 genes. We identified known mutations and some potentially pathogenic variants in each of these genes in specific cases, suggesting that their screening improves molecular diagnosis for the disorder. However, the majority of HM patients were found not to have candidate mutations in any of the previously reported HM genes, suggesting that additional genetic factors contributing to the disorder are yet to be identified.

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