scholarly journals Sequential filtering for clinically relevant variants as a method for clinical interpretation of whole exome sequencing findings in glioma

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ege Ülgen ◽  
Özge Can ◽  
Kaya Bilguvar ◽  
Cemaliye Akyerli Boylu ◽  
Şirin Kılıçturgay Yüksel ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Analysis ◽  
Clinical Interpretation ◽  
Germline Variants ◽  
Whole Exome ◽  
Gene Level ◽  
Analysis Workflow ◽  
Tumor Mutational Burden ◽  
Diffuse Gliomas

Abstract Background In the clinical setting, workflows for analyzing individual genomics data should be both comprehensive and convenient for clinical interpretation. In an effort for comprehensiveness and practicality, we attempted to create a clinical individual whole exome sequencing (WES) analysis workflow, allowing identification of genomic alterations and presentation of neurooncologically-relevant findings. Methods The analysis workflow detects germline and somatic variants and presents: (1) germline variants, (2) somatic short variants, (3) tumor mutational burden (TMB), (4) microsatellite instability (MSI), (5) somatic copy number alterations (SCNA), (6) SCNA burden, (7) loss of heterozygosity, (8) genes with double-hit, (9) mutational signatures, and (10) pathway enrichment analyses. Using the workflow, 58 WES analyses from matched blood and tumor samples of 52 patients were analyzed: 47 primary and 11 recurrent diffuse gliomas. Results The median mean read depths were 199.88 for tumor and 110.955 for normal samples. For germline variants, a median of 22 (14–33) variants per patient was reported. There was a median of 6 (0–590) reported somatic short variants per tumor. A median of 19 (0–94) broad SCNAs and a median of 6 (0–12) gene-level SCNAs were reported per tumor. The gene with the most frequent somatic short variants was TP53 (41.38%). The most frequent chromosome-/arm-level SCNA events were chr7 amplification, chr22q loss, and chr10 loss. TMB in primary gliomas were significantly lower than in recurrent tumors (p = 0.002). MSI incidence was low (6.9%). Conclusions We demonstrate that WES can be practically and efficiently utilized for clinical analysis of individual brain tumors. The results display that NOTATES produces clinically relevant results in a concise but exhaustive manner.

scholarly journals Analysis workflow to assess de novo genetic variants from human whole-exome sequencing

2021 ◽  
Vol 2 (1) ◽  
pp. 100383
Author(s):  
Nicholas S. Diab ◽  
Spencer King ◽  
Weilai Dong ◽  
Garrett Allington ◽  
Amar Sheth ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Variants ◽  
De Novo ◽  
Whole Exome ◽  
Analysis Workflow

scholarly journals Analysis of tumor mutational burden: correlation of five large gene panels with whole exome sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Carina Heydt ◽  
Jan Rehker ◽  
Roberto Pappesch ◽  
Theresa Buhl ◽  
Markus Ball ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Large Gene ◽  
Mutational Burden ◽  
Whole Exome ◽  
Tumor Mutational Burden ◽  
Gene Panels

scholarly journals Clinical advantage of targeted sequencing for unbiased tumor mutational burden estimation in samples with low tumor purity

2020 ◽  
Vol 8 (2) ◽  
pp. e001199
Author(s):  
Tae Hee Hong ◽  
Hongui Cha ◽  
Joon Ho Shim ◽  
Boram Lee ◽  
Jongsuk Chung ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Predictive Ability ◽  
Progression Free Survival ◽  
Superior Performance ◽  
Enhanced Sensitivity ◽  
Mutational Burden ◽  
Tumor Purity ◽  
Whole Exome ◽  
Tumor Mutational Burden

BackgroundTumor mutational burden (TMB) measurement is limited by low tumor purity of samples, which can influence prediction of the immunotherapy response, particularly when using whole-exome sequencing-based TMB (wTMB). This issue could be overcome by targeted panel sequencing-based TMB (pTMB) with higher depth of coverage, which remains unexplored.MethodsWe comprehensively reanalyzed four public datasets of immune checkpoint inhibitor (ICI)-treated cohorts (adopting pTMB or wTMB) to test each biomarker’s predictive ability for low purity samples (cut-off: 30%). For validation, paired genomic profiling with the same tumor specimens was performed to directly compare wTMB and pTMB in patients with breast cancer (paired-BRCA, n=165) and ICI-treated patients with advanced non-small-cell lung cancer (paired-NSCLC, n=156).ResultsLow tumor purity was common (range 30%–45%) in real-world samples from ICI-treated patients. In the survival analyzes of public cohorts, wTMB could not predict the clinical benefit of immunotherapy when tumor purity was low (log-rank p=0.874), whereas pTMB could effectively stratify the survival outcome (log-rank p=0.020). In the paired-BRCA and paired-NSCLC cohorts, pTMB was less affected by tumor purity, with significantly more somatic variants identified at low allele frequency (p<0.001). We found that wTMB was significantly underestimated in low purity samples with a large proportion of clonal variants undetected by whole-exome sequencing. Interestingly, pTMB more accurately predicted progression-free survival (PFS) after immunotherapy than wTMB owing to its superior performance in the low tumor purity subgroup (p=0.054 vs p=0.358). Multivariate analysis revealed pTMB (p=0.016), but not wTMB (p=0.32), as an independent predictor of PFS even in low-purity samples. The net reclassification index using pTMB was 21.7% in the low-purity subgroup (p=0.016).ConclusionsOur data suggest that TMB characterization with targeted deep sequencing might have potential strength in predicting ICI responsiveness due to its enhanced sensitivity for hard-to-detect variants at low-allele fraction. Therefore, pTMB could act as an invaluable biomarker in the setting of both clinical trials and practice outside of trials based on its reliable performance in mitigating the purity-related bias.

scholarly journals The combination of whole‐exome sequencing and clinical analysis allows better diagnosis of rare syndromic retinal dystrophies

2019 ◽  
Vol 97 (6) ◽  
Author(s):  
Alaa Abu Diab ◽  
Ala'a AlTalbishi ◽  
Boris Rosin ◽  
Moien Kanaan ◽  
Lara Kamal ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Analysis ◽  
Retinal Dystrophies ◽  
Whole Exome

scholarly journals Integrated Somatic and Germline Whole-Exome Sequencing Analysis in Women with Lung Cancer after a Previous Breast Cancer

Cancers ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 441 ◽  
Author(s):  
Simona Coco ◽  
Silvia Bonfiglio ◽  
Davide Cittaro ◽  
Irene Vanni ◽  
Marco Mora ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Lung Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Smoking Habit ◽  
Cancer Control ◽  
Sequencing Analysis ◽  
Multiple Cancer ◽  
Germline Variants ◽  
Whole Exome

Women treated for breast cancer (BC) are at risk of developing secondary tumors, such as lung cancer (LC). Since rare germline variants have been linked to multiple cancer development, we hypothesized that BC survivors might be prone to develop LC as a result of harboring rare variants. Sixty patients with LC with previous BC (the study population; SP) and 53 women with either BC or LC and no secondary cancer (control population; CP) were enrolled. Whole exome sequencing was performed in both tumors and unaffected tissues from 28/60 SP patients, and in germline DNA from 32/53 CP. Candidate genes were validated in the remaining individuals from both populations. We found two main mutational signature profiles: S1 (C>T) in all BCs and 16/28 LCs, and S2 (C>A) which is strongly associated with smoking, in 12/28 LCs. The burden test over rare germline variants in S1-LC vs CP identified 248 genes. Validation confirmed GSN as significantly associated with LC in never-smokers. In conclusion, our data suggest two signatures involved in LC onset in women with previous BC. One of these signatures is linked to smoking. Conversely, regardless of smoking habit, in a subgroup of BC survivors genetic susceptibility may contribute to LC risk.

Rare tumor with matched germline whole exome sequencing to identify somatic and inherited variants of clinical significance.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 1523-1523
Author(s):  
Bryce Perkins ◽  
Ryan Sprissler ◽  
Hani M. Babiker ◽  
Pavani Chalasani ◽  
Laurel Johnstone ◽  
...  
Keyword(s):  
Targeted Therapy ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Significance ◽  
The Body ◽  
Rare Tumor ◽  
Germline Variants ◽  
Rare Tumors ◽  
Whole Exome ◽  
Line Of Therapy

1523 Background: Rare cancer incidence is defined as <6/100,000 cases. These cases are challenging due to delays in diagnosis, late stage at diagnosis, lack of standard of care and poor outcomes. We present molecular profiling of 28 rare tumor cases analyzed by whole exome sequencing (WES) seen in the Early Phase Therapeutics Program. Methods: We performed WES on 15 rare tumors with matched germline DNA, as well as tumor only on 2 additional cases. We sequenced a panel of 500 candidate cancer genes in 6 tumor/normal and 6 tumor only cases. Copy number alterations (CNAs) were assessed for the tumor-normal WES cases with SNVs and small indels for all cases. Caris (AZ) (tumor only) and liquid biopsy (Gaurdant360, CA) were also conducted in these patients for comparison. Results: Rare tumors affected 18 different tissues of the body with 1 case affecting tissue typical of common cancers. The rare tumor group contained 25% pathogenic or likely pathogenic germline variants compared to 7.1% for common tumors. This increased rate of inherited pathogenic variants met statistical significance: Fisher exact test (p = 0.0118). A total of 69 sequence variants and 8 CNAs were identified, 37 were actionable. For all but 3 patients, there was at least one variant associated with an actionable outcome given off-label use or clinical trial participation. There was excellent concordance with results from commercial sequencing; however, our tumor/germline sequencing identified additional germline variants of clinical significance, all were loss-of-function variants in tumor suppressors. Tumor vs. normal analysis showed that the majority of the commercially reported VUS were in fact germline VUS. In one case, a reported pathogenic variant we found to be an inherited pathogenic germline variant. 15 patients received at least 1 line of therapy indicated by genomic sequencing. For these patients the PFS ratio when compared to the most recent line of therapy prior to targeted therapy was 2.02, with 10/15 (67%) patients having a PFS ratio of >1.0, and 6/15 (40%) of patients having PFS ratio >1.3. Conclusions: We demonstrate the importance of tumor-normal analysis, especially in the context of rare tumors. Rare tumor patients may disproportionately benefit from tumor vs. normal WES at diagnosis to improve PFS within targeted therapy trials, guided by genomics.

scholarly journals Germline whole exome sequencing of a family with appendiceal mucinous tumours presenting with pseudomyxoma peritonei

2019 ◽  
Author(s):  
Mei Sim Lung ◽  
Catherine A. Mitchell ◽  
Maria A. Doyle ◽  
Andrew C. Lynch ◽  
Kylie L. Gorringe ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Splice Site ◽  
Pseudomyxoma Peritonei ◽  
Loss Of Function ◽  
Site Mutation ◽  
Germline Variants ◽  
Missense Variants ◽  
Whole Exome ◽  
Mucinous Tumours

Abstract Background Familial cases of appendiceal mucinous tumours (AMTs) are extremely rare and the underlying genetic aetiology uncertain. We identified potential predisposing germline genetic variants in a father and daughter with AMTs presenting with pseudomyxoma peritonei (PMP) and correlated these with regions of loss of heterozygosity (LOH) in the tumours. Materials and Methods Through germline whole exome sequencing, we identified novel heterozygous loss-of-function (LoF) (i.e. nonsense, frameshift and essential splice site mutations) and missense variants shared between father and daughter, and validated all LoF variants, and missense variants with a Combined Annotation Dependent Depletion (CADD) scaled score of ≥10. Genome-wide copy number analysis was performed on tumour tissue from both individuals to identify regions of LOH. Results Seventeen novel variants in 17 genes were shared by the father and daughter: a nonsense mutation in REEP5 , an essential splice site mutation in THOP1 , and 15 missense variants. None of these germline variants were located in tumour regions of LOH shared by the father and daughter. Four genes ( EXOG , RANBP2, RANBP6 and TNFRSF1B ) harboured missense variants that fell in a region of LOH in the tumour from the father only, but none showed somatic loss of the wild type allele in the tumour. The REEP5 gene was sequenced in 23 individuals with presumed sporadic PMP; no LoF or rare missense germline variants were identified. Conclusion Germline exome sequencing of a father and daughter with AMTs identified novel candidate predisposing genes. Further studies are required to clarify the role of these genes in familial AMTs.

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