scholarly journals In silico analysis of BRCA1 and BRCA2 missense variants and the relevance in molecular genetic testing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kok-Siong Poon
Keyword(s):  
Genetic Testing ◽  
Molecular Genetic ◽  
In Silico Analysis ◽  
Molecular Testing ◽  
Brca1 And Brca2 ◽  
Missense Variants ◽  
Variants Of Unknown Significance ◽  
Sorting Intolerant From Tolerant ◽  
Unknown Significance ◽  
High Concordance

AbstractOver the years since the genetic testing of BRCA1 and BRCA2 has been conducted for research and later introduced into clinical practice, a high number of missense variants have been reported in the literature and deposited in public databases. Polymorphism Phenotyping v2 (PolyPhen-2) and Sorting Intolerant from Tolerant (SIFT) are two widely applied bioinformatics tools used to assess the functional impacts of missense variants. A total of 2605 BRCA1 and 4763 BRCA2 variants from the ClinVar database were analysed with PolyPhen2 and SIFT. When SIFT was evaluated alongside PolyPhen-2 HumDiv and HumVar, it had shown top performance in terms of negative predictive value (NPV) (100%) and sensitivity (100%) for ClinVar classified benign and pathogenic BRCA1 variants. Both SIFT and PolyPhen-2 HumDiv achieved 100% NPV and 100% sensitivity in prediction of pathogenicity of the BRCA2 variants. Agreement was achieved in prediction outcomes from the three tested approaches in 55.04% and 68.97% of the variants of unknown significance (VUS) for BRCA1 and BRCA2, respectively. The performances of PolyPhen-2 and SIFT in predicting functional impacts varied across the two genes. Due to lack of high concordance in prediction outcomes among the two tested algorithms, their usefulness in classifying the pathogenicity of VUS identified through molecular testing of BRCA1 and BRCA2 is hence limited in the clinical setting.

The incidence of BRCA1 and BRCA2 variants of unknown significance varies in different ethnic populations

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 10002-10002 ◽  
Author(s):  
D. M. Opatt ◽  
M. Morrow ◽  
M. Daly
Keyword(s):  
Breast Cancer ◽  
African American ◽  
Genetic Testing ◽  
African American Women ◽  
White Women ◽  
Personal History ◽  
Brca1 And Brca2 ◽  
Variants Of Unknown Significance ◽  
Unknown Significance ◽  
History Of

10002 Background: BRCA1 and BRCA2 mutations in the general population are rare. Women with these mutations have a significantly increased risk of invasive breast and ovarian cancer (65–85% and 15–65% cumulative lifetime risk, respectively). Variants of unknown significance (VUS), which are of uncertain clinical importance, account for up to 50% of all identified BRCA1 and BRCA2 sequence alterations1. Methods: Pooled data from all patients presenting to Fox Chase Cancer Center for genetic counseling was examined. Patients underwent genetic testing after detailed genetic counseling. Clinical data, including gender, ethnic background, and personal history of cancer, and total number of patients tested were collected. Results: A total of 1,765 women and 236 men underwent genetic testing. The distribution of ethnicity was: <1% Asian, 2.7% African American, <1% Hispanic, 2.4% other or of more than one ethnicity, 83% White, and 11% unknown. Mutations of BRCA1 and BRCA2 were seen in 13% of the women and 2.7% of the men. VUS were seen in 6.2% of the women and .15% of the men. Of the women positive for a VUS, 2.4% were Asian, 18.1% were African American, 5.5% were Hispanic, 4.7% were more than one ethnicity, 66.9% were White, and 2.4% were Unknown ethnicity. Only .15% of the men tested were positive for a VUS, all of whom were White. Of the 51 African American women tested, 45.1% were positive for a VUS while only 5.5% of the 1,503 White women tested were positive (p<0.0001). Of the females testing positive for a VUS, a personal history of breast cancer was seen in 66.7% of Asians, 78.3% of African Americans, 100% of Hispanics, 83.3% of those more than one race, 61% of Whites, and none of the people of unknown ethnic origin. One of three men testing positive for a VUS reported a history of breast cancer. Conclusions: Identification of VUS occurred disproportionately in African Americans, occurring ten times more often in African American women than White women in our study. Studies to improve classification of VUS as deleterious or neutral are needed to enhance the utility of genetic testing for women at risk, particularly those of African American ethnicity. 1Goldman, DE et al. Am. J. Hum. Genet., 2004. No significant financial relationships to disclose.

scholarly journals A functional assay to classify ZBTB24 missense variants of unknown significance

2019 ◽  
Vol 40 (8) ◽  
pp. 1077-1083 ◽  
Author(s):  
Haoyu Wu ◽  
Kelly K. D. Vonk ◽  
Silvère M. Maarel ◽  
Gijs W.E. Santen ◽  
Lucia Daxinger
Keyword(s):  
Functional Assay ◽  
Missense Variants ◽  
Variants Of Unknown Significance ◽  
Unknown Significance

scholarly journals Novel mutations in NOTCH2 gene in infants with neonatal cholestasis

2019 ◽  
Vol 11 (3) ◽  
Author(s):  
Eliana Shaul ◽  
Debora Kogan-Liberman ◽  
Stephanie Schuckalo ◽  
Dominique Jan ◽  
Michelle Ewart ◽  
...  
Keyword(s):  
Case Series ◽  
Alagille Syndrome ◽  
Notch Signaling Pathway ◽  
Clinical Approach ◽  
Neonatal Cholestasis ◽  
Retrospective Case ◽  
Variants Of Unknown Significance ◽  
Intrahepatic Bile Ducts ◽  
Sorting Intolerant From Tolerant ◽  
Unknown Significance

One cause of neonatal cholestasis (NC) is paucity of intrahepatic bile ducts which can be associated with Alagille syndrome or non- syndromic. Alagille syndrome is caused by autosomal dominant mutations in the Notch signaling pathway ligand Jagged1 in 94% of patients and mutations in the NOTCH2 receptor in <1% of patients. This is a retrospective case series studying infants with neonatal cholestasis found to have variants of unknown significance (VOUS) in NOTCH2. Sorting intolerant from tolerant (SIFT) and polymorphism phenotyping (PolyPhen) were utilized to predict a damaging effect. Five infants with NC without other features of Alagille syndrome were found to have one copy of a VOUS in NOTCH2, predicted to be damaging by SIFT and PolyPhen. Our cases support the notion that NOTCH2 mutations may result in hypoplastic biliary system. Further characterization of these variants is important to assist with our clinical approach to NC.

scholarly journals Systematic analysis of PINK1 variants of unknown significance shows intact mitophagy function for most variants

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Kai Yu Ma ◽  
Michiel R. Fokkens ◽  
Teus van Laar ◽  
Dineke S. Verbeek
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Missense Variant ◽  
Population Based ◽  
Loss Of Function ◽  
Systematic Analysis ◽  
Missense Variants ◽  
Variants Of Unknown Significance ◽  
Disease Case ◽  
Unknown Significance

AbstractPathogenic variants in PINK1 cause early-onset Parkinson’s disease. Although many PINK1 variants have been reported, the clinical significance is uncertain for the majority of them. To gain insights into the consequences of PINK1 missense variants in a systematic manner, we selected 50 PINK1 missense variants from patient- and population-wide databases and systematically classified them using Sherloc, a comprehensive framework for variant interpretation based on ACMG-AMP guidelines. We then performed functional experiments, including mitophagy and Parkin recruitment assays, to assess the downstream consequences of PINK1 variants. Analysis of PINK1 missense variants based on Sherloc showed that the patient databases over-annotate variants as likely pathogenic. Furthermore, our study shows that pathogenic PINK1 variants are most often linked to a loss-of-function for mitophagy and Parkin recruitment, while this is not observed for variants of unknown significance. In addition to the Sherloc framework, the added layer of evidence of our functional tests suggests a reclassification of 9/50 missense variants. In conclusion, we suggest the assessment of multiple layers of evidence, including functional data on top of available clinical and population-based data, to support the clinical classification of a variant and show that the presence of a missense variant in PINK1 in a Parkinson’s disease case does not automatically imply pathogenicity.

scholarly journals Comprehensive Geno- and Phenotyping in a Complex Pedigree Including Four Different Inherited Retinal Dystrophies

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 137
Author(s):  
Johannes Birtel ◽  
Martin Gliem ◽  
Kristina Hess ◽  
Theresa H. Birtel ◽  
Frank G. Holz ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Night Blindness ◽  
Molecular Genetic ◽  
Cone Dystrophy ◽  
Molecular Testing ◽  
Congenital Stationary Night Blindness ◽  
Molecular Genetic Testing ◽  
Inherited Retinal Dystrophies ◽  
Retinal Dystrophies ◽  
Novel Variant

Inherited retinal dystrophies (IRDs) are characterized by high clinical and genetic heterogeneity. A precise characterization is desirable for diagnosis and has impact on prognosis, patient counseling, and potential therapeutic options. Here, we demonstrate the effectiveness of the combination of in-depth retinal phenotyping and molecular genetic testing in complex pedigrees with different IRDs. Four affected Caucasians and two unaffected relatives were characterized including multimodal retinal imaging, functional testing, and targeted next-generation sequencing. A considerable intrafamilial phenotypic and genotypic heterogeneity was identified. While the parents of the index family presented with rod-cone dystrophy and ABCA4-related retinopathy, their two sons revealed characteristics in the spectrum of incomplete congenital stationary night blindness and ocular albinism, respectively. Molecular testing revealed previously described variants in RHO, ABCA4, and MITF as well as a novel variant in CACNA1F. Identified variants were verified by intrafamilial co-segregation, bioinformatic annotations, and in silico analysis. The coexistence of four independent IRDs caused by distinct mutations and inheritance modes in one pedigree is demonstrated. These findings highlight the complexity of IRDs and underscore the need for the combination of extensive molecular genetic testing and clinical characterization. In addition, a novel variant in the CACNA1F gene is reported associated with incomplete congenital stationary night blindness.

Impact Analysis of Missense Variants of Unknown Significance Using the TRPV4 Protein as a Model: A Study Guide

2021 ◽  
pp. 95-105
Author(s):  
Ligia Silva Pondé Serra ◽  
Juliane da Silva Ferreira ◽  
Kamila de Oliveira e Silva ◽  
Sérgio Amorim de Alencar
Keyword(s):  
Impact Analysis ◽  
Study Guide ◽  
Missense Variants ◽  
Variants Of Unknown Significance ◽  
Unknown Significance

scholarly journals Functional assessment of variants associated with Wolfram syndrome

2019 ◽  
Vol 28 (22) ◽  
pp. 3815-3824
Author(s):  
Melissa Riachi ◽  
Sebahat Yilmaz ◽  
Erdal Kurnaz ◽  
Zehra Aycan ◽  
Semra Çetinkaya ◽  
...  
Keyword(s):  
Neurodegenerative Disorder ◽  
Molecular Genetic ◽  
Wolfram Syndrome ◽  
Neurological Complications ◽  
Variants Of Unknown Significance ◽  
Pathogenic Variants ◽  
Unknown Significance ◽  
Genetic Mechanisms ◽  
Allelic Variations

Abstract Wolfram syndrome (WS) is a heterogeneous multisystem neurodegenerative disorder with two allelic variations in addition to a separate subtype known as WS type 2. The wide phenotypic spectrum of WS includes diabetes mellitus and optic atrophy which is often accompanied by diabetes insipidus, deafness, urological and neurological complications in combination or in isolation. To date, the understanding of the genotype-phenotype relationship in this complex syndrome remains poorly understood. In this study, we identified and explored the functionality of rare and novel variants in the two causative WS genes WFS1 and CISD2 by assessing the effects of the mutations on the encoded proteins Wolframin and ERIS, in a cohort of 12 patients with autosomal recessive WS, dominant WS and WS type 2. The identified pathogenic variants included missense changes, frameshift deletions and insertions in WFS1 and an exonic deletion in CISD2 which all altered the respective encoded protein in a manner that did not correlate to the phenome previously described. These observations suggest the lack of genotype-phenotype correlation in this complex syndrome and the need to explore other molecular genetic mechanisms. Additionally, our findings highlight the importance of functionally assessing variants for their pathogenicity to tackle the problem of increasing variants of unknown significance in the public genetic databases.

Classification of missense variants of unknown significance inBRCA1based on clinical and tumor information

2007 ◽  
Vol 28 (5) ◽  
pp. 477-485 ◽  
Author(s):  
A. Osorio ◽  
R.L. Milne ◽  
E. Honrado ◽  
A. Barroso ◽  
O. Diez ◽  
...  
Keyword(s):  
Missense Variants ◽  
Variants Of Unknown Significance ◽  
Unknown Significance

scholarly journals Facilitations and Hurdles of Genetic Testing in Neuromuscular Disorders

Diagnostics ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 701
Author(s):  
Andrea Barp ◽  
Lorena Mosca ◽  
Valeria Ada Sansone
Keyword(s):  
Genetic Testing ◽  
Neuromuscular Disorders ◽  
Single Nucleotide Variants ◽  
Gene Therapies ◽  
Variants Of Unknown Significance ◽  
Unknown Significance ◽  
New Gene ◽  
Genetic Techniques ◽  
Definition Of ◽  
Next Generation Sequencing Ngs

Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of “unknown significance” can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain “not genetically defined”. In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss “facilitations and hurdles” of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of “therapeutic offer”.

scholarly journals The underestimated burden of monogenic kidney disease in adults waitlisted for kidney transplantation

2021 ◽  
Author(s):  
Eva Schrezenmeier ◽  
Elisa Kremerskothen ◽  
Fabian Halleck ◽  
Oliver Staeck ◽  
Lutz Liefeldt ◽  
...  
Keyword(s):  
Kidney Transplantation ◽  
Genetic Testing ◽  
Kidney Disease ◽  
Diagnostic Value ◽  
Considerable Proportion ◽  
Major Health ◽  
Variants Of Unknown Significance ◽  
Health Care Burden ◽  
Unknown Significance ◽  
Next Generation Sequencing Ngs

Abstract Purpose Chronic kidney disease (CKD) is a major health-care burden. Increasing evidence suggests that a considerable proportion of patients are affected by a monogenic kidney disorder. Methods In this study, the kidney transplantation waiting list at the Charité was screened for patients with undetermined cause of CKD. By next-generation sequencing (NGS) we targeted all 600 genes described and associated with kidney disease or allied disorders. Results In total, 635 patients were investigated. Of these, 245 individuals had a known cause of CKD (38.5%) of which 119 had a proven genetic disease (e.g., ADPKD, Alport). The other 340 patients (53.5%) were classified as undetermined diagnosis, of whom 87 had kidney failure (KF) onset <40 years. To this latter group genetic testing was offered as well as to those patients (n = 29) with focal segmental glomerulosclerosis (FSGS) and all individuals (n = 21) suspicious for thrombotic microangiopathy (TMA) in kidney biopsy. We detected diagnostic variants in 26 of 126 patients (20.6%) of which 14 of 126 (11.1%) were pathogenic or likely pathogenic. In another 12 of 126 (9.5%) patients, variants of unknown significance (VUS) were detected. Conclusion Our study demonstrates the diagnostic value of comprehensive genetic testing among patients with undetermined CKD.

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