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 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 High Diagnostic Yield of Whole Exome Sequencing in Participants With Retinal Dystrophies in a Clinical Ophthalmology Setting

2015 ◽  
Vol 160 (2) ◽  
pp. 354-363.e9 ◽  
Author(s):  
Kristy Lee ◽  
Jonathan S. Berg ◽  
Laura Milko ◽  
Kristy Crooks ◽  
Mei Lu ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Diagnostic Yield ◽  
High Diagnostic Yield ◽  
Retinal Dystrophies ◽  
Whole Exome

scholarly journals Whole exome sequencing and homozygosity mapping reveals genetic defects in consanguineous Iranian families with inherited retinal dystrophies

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Arash Salmaninejad ◽  
Nicola Bedoni ◽  
Zeinab Ravesh ◽  
Mathieu Quinodoz ◽  
Nasser Shoeibi ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Snp Array ◽  
Homozygosity Mapping ◽  
Retinal Cell ◽  
Additional Information ◽  
Inherited Retinal Dystrophies ◽  
Pathogenic Variants ◽  
Retinal Dystrophies ◽  
Whole Exome

Abstract Inherited retinal dystrophies (IRDs), displaying pronounced genetic and clinical heterogeneity, comprise of a broad range of diseases characterized by progressive retinal cell death and gradual loss of vision. By the combined use of whole exome sequencing (WES), SNP-array and WES-based homozygosity mapping, as well as directed DNA sequencing (Sanger), we have identified nine pathogenic variants in six genes (ABCA4, RPE65, MERTK, USH2A, SPATA7, TULP1) in 10 consanguineous Iranian families. Six of the nine identified variants were novel, including a putative founder mutation in ABCA4 (c.3260A>G, p.Glu1087Gly), detected in two families from Northeastern Iran. Our findings provide additional information to the molecular pathology of IRDs in Iran, hopefully contributing to better genetic counselling and patient management in the respective families from this country.

scholarly journals Whole exome sequencing using Ion Proton system enables reliable genetic diagnosis of inherited retinal dystrophies

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Marina Riera ◽  
Rafael Navarro ◽  
Sheila Ruiz-Nogales ◽  
Pilar Méndez ◽  
Anniken Burés-Jelstrup ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Diagnosis ◽  
Inherited Retinal Dystrophies ◽  
Retinal Dystrophies ◽  
Whole Exome ◽  
Ion Proton

scholarly journals Identification of Novel and Recurrent Disease-Causing Mutations in Retinal Dystrophies Using Whole Exome Sequencing (WES): Benefits and Limitations

PLoS ONE ◽  
2016 ◽  
Vol 11 (7) ◽  
pp. e0158692 ◽  
Author(s):  
Amit Tiwari ◽  
Johannes Lemke ◽  
Janine Altmueller ◽  
Holger Thiele ◽  
Esther Glaus ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Recurrent Disease ◽  
Retinal Dystrophies ◽  
Whole Exome

Gene mutation and clinical analysis of nephronophthisis diagnosed using whole exome sequencing: Experience from China

2019 ◽  
Vol 92 (2) ◽  
pp. 89-94 ◽  
Author(s):  
Xiaoshan Tang ◽  
Hong Xu ◽  
Qian Shen ◽  
Guoming Li ◽  
Jia Rao ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Gene Mutation ◽  
Whole Exome Sequencing ◽  
Clinical Analysis ◽  
Whole Exome

scholarly journals Whole exome sequencing reveals putatively novel associations in retinopathies and drusen formation

2021 ◽  
Author(s):  
Lance P. Doucette ◽  
Nicole C. L. Noel ◽  
Yi Zhai ◽  
Manlong Xu ◽  
Oana Caluseriu ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Research Setting ◽  
Genetic Etiology ◽  
Inherited Retinal Dystrophies ◽  
Retinal Dystrophies ◽  
Clinical Investigations ◽  
Whole Exome ◽  
Disease Associated Genes ◽  
Novel Associations

AbstractInherited retinal dystrophies (IRDs) affect 1 in 3000 individuals worldwide and are genetically heterogeneous, with over 270 identified genes and loci; however, there are still many identified disorders with no current genetic etiology. Whole exome sequencing (WES) provides a hypothesis-free first examination of IRD patients in either a clinical or research setting to identify the genetic cause of disease. We present a study of IRD in ten families from Alberta, Canada, through the lens of novel gene discovery. We identify the genetic etiology of IRDs in three of the families to be variants in known disease-associated genes, previously missed by clinical investigations. In addition, we identify two potentially novel associations: LRP1 in early-onset drusen formation and UBE2U in a multi-system condition presenting with retinoschisis, cataracts, learning disabilities, and developmental delay. We also describe interesting results in our unsolved cases to provide further information to other investigators of these blinding conditions.

Whole Exome Sequencing (WES) in Familien mit linksventrikulärer Ausfluβtraktobstruktion (LVOTO)

2014 ◽  
Vol 62 (S 02) ◽  
Author(s):  
M. Hitz ◽  
S. Al-Turki ◽  
A. Schalinski ◽  
U. Bauer ◽  
T. Pickardt ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome

FV 1031. Whole Exome Sequencing for Children with Dyskinetic Movement Disorder

2018 ◽  
Author(s):  
Yasemin Dincer ◽  
Michael Zech ◽  
Matias Wagner ◽  
Nikolai Jung ◽  
Volker Mall ◽  
...  
Keyword(s):  
Movement Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Dyskinetic Movement
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