HGG-21. GERMLINE MUTATIONS IN MSH2 GENE IN PEDIATRIC PATIENTS WITH CONGENITAL AND SPORADIC GLIOBLASTOMA

Abstract INTRODUCTION Glioblastoma (GBM) remains one of the biggest therapeutic challenges in neuro-oncology. In spite of multimodal treatment approaches the prognosis of GBM is extremely poor, median survival is estimated about 12–16 months. Although GBM is one of the most common and malignant primary brain tumors, pediatric glioblastoma, including congenital is a very rare tumor, with an incidence of about 1.1–3.4 per million live births. Moreover, the mode of presentation, behavior, response to therapy and molecular background of pediatric glioblastomas differs from adult type of GBM. Until now, about ten patients with congenital glioblastoma have been described and in none of them germline markers were examined. Here we report two patients with GBM, one with congenital tumor with germline mutations in MSH2 gene. METHODS Targeted Next-Generation Sequencing (NGS) of the probands DNA extracted from leucocytes was performed using the TruSight One sequencing panel on an Illumina HiSeq 1500. Applied gene panel investigated the coding sequence and splice sites of 4813 genes associated with known disease phenotypes. The NGS data were analyzed using an in-house procedure. Identified variants were validated by Sanger sequencing. RESULTS NGS analysis of patients constitutional DNA revealed know, pathogenic variants c.940C>T and c.942 + 3A>T in MSH2 gene (NM_000251.3) associated with MMR-dependent hereditary cancer syndromes. CONCLUSION Molecular analysis are heavily needed for better understanding of pediatric GBM etiology and new treatment modality implementation. Identification of this oncogenic driver may provide insight into the pathogenesis of GBM, including congenital cases. Funded by National Science Centre, Poland (2016/23/B/NZ2/03064 and 2016/21/B/NZ2/01785).

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The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data

Wellcome Open Research ◽

10.12688/wellcomeopenres.11689.1 ◽

2017 ◽

Vol 2 ◽

pp. 35 ◽

Cited By ~ 7

Author(s):

Shazia Mahamdallie ◽

Elise Ruark ◽

Shawn Yost ◽

Emma Ramsay ◽

Imran Uddin ◽

...

Keyword(s):

Sequencing Data ◽

Targeted Next Generation Sequencing ◽

Negative Results ◽

Targeted Ngs ◽

Predisposition Genes ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Validation Series ◽

Generation Sequencing ◽

Dependent Probe

Detection of deletions and duplications of whole exons (exon CNVs) is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS) data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results. This hinders tool comparisons, transparency and reproducibility. To provide a community resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM or PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs, the most difficult type of exon CNV to detect. The FASTQ files for the ICR96 exon CNV validation series can be accessed through the European-Genome phenome Archive (EGA) under the accession number EGAS00001002428.

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Genetic Variants Detected Using Cell-Free DNA from Blood and Tumor Samples in Patients with Inflammatory Breast Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms21041290 ◽

2020 ◽

Vol 21 (4) ◽

pp. 1290

Author(s):

Jennifer S. Winn ◽

Zachary Hasse ◽

Michael Slifker ◽

Jianming Pei ◽

Sebastian M. Arisi-Fernandez ◽

...

Keyword(s):

Breast Cancer ◽

Inflammatory Breast Cancer ◽

Triple Negative ◽

Genetic Profile ◽

Cell Free Dna ◽

Targeted Next Generation Sequencing ◽

Pathogenic Variants ◽

Free Dna ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

We studied genomic alterations in 19 inflammatory breast cancer (IBC) patients with advanced disease using samples of tissue and paired blood serum or plasma (cell-free DNA, cfDNA) by targeted next generation sequencing (NGS). At diagnosis, the disease was triple negative (TN) in eleven patients (57.8%), ER+ Her2- IBC in six patients (31.6%), ER+ Her2+ IBC in one patient (5.3%), and ER- Her2+ IBC in one other patient (5.3%). Pathogenic or likely pathogenic variants were frequently detected in TP53 (47.3%), PMS2 (26.3%), MRE11 (26.3%), RB1 (10.5%), BRCA1 (10.5%), PTEN (10.5%) and AR (10.5%); other affected genes included PMS1, KMT2C, BRCA2, PALB2, MUTYH, MEN1, MSH2, CHEK2, NCOR1, PIK3CA, ESR1 and MAP2K4. In 15 of the 19 patients in which tissue and paired blood were collected at the same time point, 80% of the variants detected in tissue were also detected in the paired cfDNA. Higher concordance between tissue and cfDNA was found for variants with higher allele fraction in tissue (AFtissue ≥ 5%). Furthermore, 86% of the variants detected in cfDNA were also detected in paired tissue. Our study suggests that the genetic profile measured in blood cfDNA is complementary to that of tumor tissue in IBC patients.

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Targeted next generation sequencing in patients with maturity-onset diabetes of the young (MODY)

Journal of Pediatric Endocrinology and Metabolism ◽

10.1515/jpem-2018-0184 ◽

2018 ◽

Vol 31 (12) ◽

pp. 1295-1304 ◽

Cited By ~ 6

Author(s):

Taha R. Özdemir ◽

Özgür Kırbıyık ◽

Bumin N. Dündar ◽

Ayhan Abacı ◽

Özge Ö. Kaya ◽

...

Keyword(s):

Next Generation Sequencing ◽

Maturity Onset Diabetes ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Pathogenic Variants ◽

Onset Diabetes ◽

Frequent Mutations ◽

Standards And Guidelines ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Background Maturity-onset diabetes of the young (MODY) is a common form of monogenic diabetes. Fourteen genes have been identified, each leading to cause a different type of MODY. The aims of this study were to reveal both known and novel variants in MODY genes in patients with MODY using targeted next generation sequencing (NGS) and to present the genotype-phenotype correlations. Methods Mutation analysis of MODY genes (GCK, HNF1A, HNF4A, HNF1B, ABCC8, INS and KCNJ11) was performed using targeted NGS in 106 patients with a clinical diagnosis of MODY. The variants were evaluated according to American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines recommendations. Results A total of 18 (17%) variants were revealed among all patients. Seven variants in GCK, six in HNF4A, four in HNF1A and one in ABCC8 genes were found. Eight of them were previously published and 10 of them were assessed as novel pathogenic or likely pathogenic variants. Conclusions While the most frequent mutations are found in the HNF1A gene in the literature, most of the variants were found in the GCK gene in our patient group using the NGS method, which allows simultaneous analysis of multiple genes in a single panel.

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Detection and validation of six pathogenic variants in Chinese inherited heart disease patients using clinical whole-exome sequencing

10.22541/au.162566292.28770313/v1 ◽

2021 ◽

Author(s):

Lichao Cao ◽

Fei Ye ◽

Shuqi Xie ◽

Ying Ba ◽

Ying Zeng ◽

...

Keyword(s):

Heart Disease ◽

Next Generation Sequencing ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Sanger Sequencing ◽

Targeted Next Generation Sequencing ◽

Pathogenic Variants ◽

Whole Exome ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

The targeted next-generation sequencing (NGS) was employed in detecting the pathogenic mutations in inherited heart disease patients in the present study. Two main methods, the NGS and the classic Sanger sequencing, were used in this study. And, the whole-exome sequencing (WES) was specifically used in this study.

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Allele frequency analysis of variants reported to cause autosomal dominant inherited retinal diseases question the involvement of 19% of genes and 10% of reported pathogenic variants

Journal of Medical Genetics ◽

10.1136/jmedgenet-2018-105971 ◽

2019 ◽

Vol 56 (8) ◽

pp. 536-542 ◽

Cited By ~ 4

Author(s):

Mor Hanany ◽

Dror Sharon

Keyword(s):

Allele Frequency ◽

Autosomal Dominant ◽

Warning Sign ◽

Retinal Diseases ◽

Inheritance Pattern ◽

Pathogenic Variants ◽

Mutation Database ◽

Next Generation Sequencing Ngs ◽

Functional Analyses ◽

Ngs Data

BackgroundNext generation sequencing (NGS) generates a large amount of genetic data that can be used to better characterise disease-causing variants. Our aim was to examine allele frequencies of sequence variants reported to cause autosomal dominant inherited retinal diseases (AD-IRDs).MethodsGenetic information was collected from various databases, including PubMed, the Human Genome Mutation Database, RETNET and gnomAD.ResultsWe generated a database of 1223 variants reported in 58 genes, including their allele frequency in gnomAD that contains NGS data of over 138 000 individuals. While the majority of variants are not represented in gnomAD, 138 had an allele count of >1 and were examined carefully for various aspects including cosegregation and functional analyses. The analysis revealed 122 variants that were reported pathogenic but unlikely to cause AD-IRDs. Interestingly, in some cases, these unlikely pathogenic variants were the only ones reported to cause disease in AD inheritance pattern for a particular gene, therefore raising doubt regarding the involvement of 11 (19%) of the genes in AD-IRDs.ConclusionWe predict that these data are not limited to a specific disease or inheritance pattern since non-pathogenic variants were mistakenly reported as pathogenic in various diseases. Our results should serve as a warning sign for geneticists, variant database curators and sequencing panels’ developers not to automatically accept reported variants as pathogenic but cross-reference the information with large databases.

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Standardization of Somatic Variant Classifications in Solid and Haematological Tumours by a Two-Level Approach of Biological and Clinical Classes: An Initiative of the Belgian ComPerMed Expert Panel

Cancers ◽

10.3390/cancers11122030 ◽

2019 ◽

Vol 11 (12) ◽

pp. 2030 ◽

Cited By ~ 2

Author(s):

Guy Froyen ◽

Marie Le Mercier ◽

Els Lierman ◽

Karl Vandepoele ◽

Friedel Nollet ◽

...

Keyword(s):

Cancer Diagnostics ◽

Reference Sequence ◽

Clinical Interpretation ◽

Subjective Analysis ◽

Targeted Next Generation Sequencing ◽

Workflow System ◽

Set Up ◽

High Consistency ◽

Next Generation Sequencing Ngs ◽

Ngs Data

In most diagnostic laboratories, targeted next-generation sequencing (NGS) is currently the default assay for the detection of somatic variants in solid as well as haematological tumours. Independent of the method, the final outcome is a list of variants that differ from the human genome reference sequence of which some may relate to the establishment of the tumour in the patient. A critical point towards a uniform patient management is the assignment of the biological contribution of each variant to the malignancy and its subsequent clinical impact in a specific malignancy. These so-called biological and clinical classifications of somatic variants are currently not standardized and are vastly dependent on the subjective analysis of each laboratory. This subjectivity can thus result in a different classification and subsequent clinical interpretation of the same variant. Therefore, the ComPerMed panel of Belgian experts in cancer diagnostics set up a working group with the goal to harmonize the biological classification and clinical interpretation of somatic variants detected by NGS. This effort resulted in the establishment of a uniform, two-level classification workflow system that should enable high consistency in diagnosis, prognosis, treatment and follow-up of cancer patients. Variants are first classified into a tumour-independent biological five class system and subsequently in a four tier ACMG clinical classification. Here, we describe the ComPerMed workflow in detail including examples for each step of the pipeline. Moreover, this workflow can be implemented in variant classification software tools enabling automatic reporting of NGS data, independent of panel, method or analysis software.

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Improving the Management of Patients with Hearing Loss by the Implementation of an NGS Panel in Clinical Practice

Genes ◽

10.3390/genes11121467 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1467

Author(s):

Gema García-García ◽

Alba Berzal-Serrano ◽

Piedad García-Díaz ◽

Rebeca Villanova-Aparisi ◽

Sara Juárez-Rodríguez ◽

...

Keyword(s):

Hearing Loss ◽

Autosomal Recessive ◽

Targeted Next Generation Sequencing ◽

Pathogenic Variants ◽

Targeted Ngs ◽

Syndromic Hearing Loss ◽

Genetics And Genomics ◽

Custom Panel ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

A cohort of 128 patients from 118 families diagnosed with non-syndromic or syndromic hearing loss (HL) underwent an exhaustive clinical evaluation. Molecular analysis was performed using targeted next-generation sequencing (NGS) with a custom panel that included 59 genes associated with non-syndromic HL or syndromic HL. Variants were prioritized according to the minimum allele frequency and classified according to the American College of Medical Genetics and Genomics guidelines. Variant(s) responsible for the disease were detected in a 40% of families including autosomal recessive (AR), autosomal dominant (AD) and X-linked patterns of inheritance. We identified pathogenic or likely pathogenic variants in 26 different genes, 15 with AR inheritance pattern, 9 with AD and 2 that are X-linked. Fourteen of the found variants are novel. This study highlights the clinical utility of targeted NGS for sensorineural hearing loss. The optimal panel for HL must be designed according to the spectrum of the most represented genes in a given population and the laboratory capabilities considering the pressure on healthcare.

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Microbiome signatures in prostate cancer

Carcinogenesis ◽

10.1093/carcin/bgz008 ◽

2019 ◽

Vol 40 (6) ◽

pp. 749-764 ◽

Cited By ~ 10

Author(s):

Sagarika Banerjee ◽

James C Alwine ◽

Zhi Wei ◽

Tian Tian ◽

Natalie Shih ◽

...

Keyword(s):

Prostate Cancer ◽

Direct Pcr ◽

Prostate Hyperplasia ◽

Targeted Next Generation Sequencing ◽

Cellular Genes ◽

Prostate Tumor Cells ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Benign Prostate ◽

Generation Sequencing

Abstract We have established a microbiome signature for prostate cancer using an array-based metagenomic and capture-sequencing approach. A diverse microbiome signature (viral, bacterial, fungal and parasitic) was observed in the prostate cancer samples compared with benign prostate hyperplasia controls. Hierarchical clustering analysis identified three distinct prostate cancer-specific microbiome signatures. The three signatures correlated with different grades, stages and scores of the cancer. Thus, microbiome signature analysis potentially provides clinical diagnosis and outcome predictions. The array data were validated by PCR and targeted next-generation sequencing (NGS). Specific NGS data suggested that certain viral genomic sequences were inserted into the host somatic chromosomes of the prostate cancer samples. A randomly selected group of these was validated by direct PCR and sequencing. In addition, PCR validation of Helicobacter showed that Helicobacter cagA sequences integrated within specific chromosomes of prostate tumor cells. The viral and Helicobacter integrations are predicted to affect the expression of several cellular genes associated with oncogenic processes.

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Peritoneal mesotheliomas characterized by less cell-cycle alterations and more TRAF7 alterations than malignant pleural mesotheliomas.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.9059 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 9059-9059

Author(s):

Michael Offin ◽

Jacklynn V. Egger ◽

Andrea Cercek ◽

Garrett Michael Nash ◽

Marc Ladanyi ◽

...

Keyword(s):

Cell Cycle ◽

Genetic Alterations ◽

Time Interval ◽

Clinicopathologic Characteristics ◽

Targeted Next Generation Sequencing ◽

Molecular Alterations ◽

Pathogenic Variants ◽

Mutation Burden ◽

Well Differentiated ◽

Next Generation Sequencing Ngs

9059 Background: While peritoneal mesotheliomas (PM) are clinically distinct from malignant pleural mesotheliomas (MPM) it is unknown if genetic alterations reflect these differences. Here we report the molecular alterations and clinicopathologic characteristics of a prospectively collected PM cohort as compared to MPM. Methods: Patients with PM (n = 59) and targeted next generation sequencing (NGS; MSK-IMPACT) from January 2014 to January 2019 were assessed and followed through February 2020. Germline variants were analyzed in consented patients. NGS was compared to patients with MPM (n = 194) assessed in the same time interval. Results: Median age at diagnosis was 61 (range: 20-77), 56% were women (n = 33), and 92% had epithelioid histology (n = 54). 66% had ascites (n = 39) and 24% developed extra-abdominal metastases (n = 14; including lung, pleura, and mediastinum). 68% (n = 40) underwent surgical debulking and 80% (n = 47) had infusional therapy (median lines: 3) including platinum/pemetrexed (n = 38), EPIC (n = 22), HIPEC (n = 15), and immunotherapy (n = 16). The median overall survival (OS) from diagnosis was 5.4 years (median follow up 3.5 years). The median tumor mutation burden (TMB) was 1.8 mut/Mb (range: 0-14.9) in PM vs 2.0 mut/Mb (range: 0-31.5) in MPM (p = 0.049). More patients with PM had TRAF7 alterations than in MPM (5/59 vs 3/194; p = 0.02) while fewer had CDKN2A/ CDKN2B (4 vs 55; p = 0.0004). All patients with TRAF7 altered PM had well-differentiated papillary epithelioid histology. There was no difference in the prevalence of other common alterations such as BAP1 (32 vs 98; p = 0.66), NF2 (12 vs 55, p = 0.24), SETD2 (11 vs 24; p = 0.28), and TP53 (9 vs 28; p = 0.84) in PM vs MPM respectively. Patients with BAP1-altered PM had shorter OS (4.6 vs 9.8 years; HR 2.6, 95% CI 1.1-6.4; p = 0.04) while TRAF7-altered PM had improved OS (not reached vs 4.8 years; HR 0.3, 95% CI 0.1-0.9; p = 0.04) compared to wild type. 13% (4/30) of patients with PM had pathogenic variants on germline NGS ( POT1 I78T, MUTYH R109Y, BAP1 E402*, APC I1037K). Conclusions: NGS confirms the distinct biology of PM compared to MPM. Specifically, the former shows fewer cell cycle ( CDKN2) alterations compared to MPM. In contrast to MPM, BAP1 alteration was associated with shorter survival. As previously described, we found enrichment of TRAF7 in well differentiated papillary epithelioid PM associated with improved survival but notably some TRAF7 alterations were identified in poorly differentiated MPM. Consistent with other reports, the prevalence of germline alterations was 13%.

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Phenocopy of a heterozygous carrier of X-linked retinitis pigmentosa due to mosaicism for a RHO variant

Scientific Reports ◽

10.1038/s41598-020-80400-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ine Strubbe ◽

Caroline Van Cauwenbergh ◽

Julie De Zaeytijd ◽

Sarah De Jaegere ◽

Marieke De Bruyne ◽

...

Keyword(s):

Retinitis Pigmentosa ◽

Somatic Mosaicism ◽

Retinal Disease ◽

Hair Follicles ◽

Disease Genes ◽

Female Carrier ◽

Autofluorescence Imaging ◽

Targeted Next Generation Sequencing ◽

Whole Exome ◽

Next Generation Sequencing Ngs

AbstractWe describe both phenotype and pathogenesis in two male siblings with typical retinitis pigmentosa (RP) and the potentially X-linked RP (XLRP) carrier phenotype in their mother. Two affected sons, two unaffected daughters, and their mother underwent detailed ophthalmological assessments including Goldmann perimetry, color vision testing, multimodal imaging and ISCEV-standard electroretinography. Genetic testing consisted of targeted next-generation sequencing (NGS) of known XLRP genes and whole exome sequencing (WES) of known inherited retinal disease genes (RetNet-WES). Variant validation and segregation analysis were performed by Sanger sequencing. The mutational load of the RHO variant in the mother was assessed in DNA from leucocytes, buccal cells and hair follicles using targeted NGS. Both affected sons showed signs of classical RP, while the mother displayed patches of hyperautofluorescence on blue light autofluorescence imaging and regional, intraretinal, spicular pigmentation, reminiscent of a carrier phenotype of XLRP. XLRP testing was negative. RetNet-WES testing revealed RHO variant c.404G > C p.(Arg135Pro) in a mosaic state (21% of the reads) in the mother and in a heterozygous state in both sons. Targeted NGQSS of the RHO variant in different maternal tissues showed a mutation load between 25.06% and 41.72%. We report for the first time that somatic mosaicism of RHO variant c.404G > C p.(Arg135Pro) mimics the phenotype of a female carrier of XLRP, in combination with heterozygosity for the variant in the two affected sons.

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