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

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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Facilitations and Hurdles of Genetic Testing in Neuromuscular Disorders

Diagnostics ◽

10.3390/diagnostics11040701 ◽

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”.

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Germline mutations in the new E1’ cryptic exon of the VHL gene in patients with tumours of von Hippel-Lindau disease spectrum or with paraganglioma

Journal of Medical Genetics ◽

10.1136/jmedgenet-2019-106519 ◽

2020 ◽

Vol 57 (11) ◽

pp. 752-759 ◽

Cited By ~ 3

Author(s):

Alexandre Buffet ◽

Bruna Calsina ◽

Shahida Flores ◽

Sophie Giraud ◽

Marion Lenglet ◽

...

Keyword(s):

Genetic Variants ◽

Diagnostic Testing ◽

Germline Mutations ◽

Cryptic Exon ◽

Von Hippel Lindau ◽

Variants Of Unknown Significance ◽

Disease Spectrum ◽

Unknown Significance ◽

Next Generation Sequencing Ngs ◽

Vhl Disease

BackgroundsThe incidence of germline mutations in the newly discovered cryptic exon (E1’) of VHL gene in patients with von Hippel-Lindau (VHL) disease and in patients with paraganglioma or pheochromocytoma (PPGL) is not currently known.MethodsWe studied a large international multicentre cohort of 1167 patients with a previous negative genetic testing. Germline DNA from 75 patients with a single tumour of the VHL spectrum (‘Single VHL tumour’ cohort), 70 patients with multiple tumours of the VHL spectrum (‘Multiple VHL tumours’ cohort), 76 patients with a VHL disease as described in the literature (‘VHL-like’ cohort) and 946 patients with a PPGL were screened for E1’ genetic variants.ResultsSix different genetic variants in E1' were detected in 12 patients. Two were classified as pathogenic, 3 as variants of unknown significance and 1 as benign. The rs139622356 was found in seven unrelated patients but described in only 16 patients out of the 31 390 of the Genome Aggregation Database (p<0.0001) suggesting that this variant might be either a recurrent mutation or a modifier mutation conferring a risk for the development of tumours and cancers of the VHL spectrum.ConclusionsVHL E1’ cryptic exon mutations contribute to 1.32% (1/76) of ‘VHL-like’ cohort and to 0.11% (1/946) of PPGL cohort and should be screened in patients with clinical suspicion of VHL, and added to panels for Next Generation Sequencing (NGS) diagnostic testing of hereditary PPGL. Our data highlight the importance of studying variants identified in deep intronic sequences, which would have been missed by examining only coding sequences of genes/exomes. These variants will likely be more frequently detected and studied with the upcoming implementation of whole-genome sequencing into clinical practice.

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Clinical Applications of Genetic Discoveries in Kidney Transplantation: a Review

Kidney360 ◽

10.34067/kid.0000312019 ◽

2020 ◽

Vol 1 (4) ◽

pp. 300-305

Author(s):

Ethan P. Marin ◽

Elizabeth Cohen ◽

Neera Dahl

Keyword(s):

Kidney Transplantation ◽

Genetic Testing ◽

Kidney Disease ◽

Kidney Transplant ◽

Clinical Applications ◽

Transplant Recipients ◽

Kidney Transplant Recipients

Growth in knowledge of the genetics of kidney disease has revealed that significant percentages of patients with diverse types of nephropathy have causative mutations. Genetic testing is poised to play an increasing role in the care of patients with kidney disease. The role of genetic testing in kidney transplantation is not well established. This review will explore the ways in which genetic testing may be applied to improve the care of kidney transplant recipients and donors.

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Targeted NGS Yields Plentiful Ultra-Rare Variants in Inborn Errors of Immunity Patients

Genes ◽

10.3390/genes12091299 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1299

Author(s):

Alice Grossi ◽

Maurizio Miano ◽

Marina Lanciotti ◽

Francesca Fioredda ◽

Daniela Guardo ◽

...

Keyword(s):

Rare Variants ◽

Causative Gene ◽

Inborn Errors ◽

Variants Of Unknown Significance ◽

Inborn Errors Of Immunity ◽

Complex Patients ◽

Unknown Significance ◽

Gene Panels ◽

Clinical Pictures ◽

Next Generation Sequencing Ngs

Inborn errors of immunity (IEI) include a large group of inherited diseases sharing either poor, dysregulated, or absent and/or acquired function in one or more components of the immune system. Next-generation sequencing (NGS) has driven a rapid increase in the recognition of such defects, though the wide heterogeneity of genetically diverse but phenotypically overlapping diseases has often prevented the molecular characterization of the most complex patients. Two hundred and seventy-two patients were submitted to three successive NGS-based gene panels composed of 58, 146, and 312 genes. Along with pathogenic and likely pathogenic causative gene variants, accounting for the corresponding disorders (37/272 patients, 13.6%), a number of either rare (probably) damaging variants in genes unrelated to patients’ phenotype, variants of unknown significance (VUS) in genes consistent with their clinics, or apparently inconsistent benign, likely benign, or VUS variants were also detected. Finally, a remarkable amount of yet unreported variants of unknown significance were also found, often recurring in our dataset. The NGS approach demonstrated an expected IEI diagnostic rate. However, defining the appropriate list of genes for these panels may not be straightforward, and the application of unbiased approaches should be taken into consideration, especially when patients show atypical clinical pictures.

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

Journal of Clinical Oncology ◽

10.1200/jco.2006.24.18_suppl.10002 ◽

2006 ◽

Vol 24 (18_suppl) ◽

pp. 10002-10002 ◽

Cited By ~ 1

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.

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Genomic alterations in 670 patients with diverse cancers analyzed by next-generation sequencing (NGS) of circulating tumor DNA (ctDNA).

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.11593 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. 11593-11593

Author(s):

Maria Clemence Schwaederle ◽

Ranajoy Chattopadhyay ◽

Shumei Kato ◽

Paul T. Fanta ◽

Kimberly Banks ◽

...

Keyword(s):

Brain Tumors ◽

Head And Neck ◽

Clinical Laboratory ◽

Circulating Tumor Dna ◽

Head And Neck Tumors ◽

Clinical Laboratory Improvement Amendment ◽

Variants Of Unknown Significance ◽

Neck Tumors ◽

Unknown Significance ◽

Next Generation Sequencing Ngs

11593 Background: NGS of blood-derived ctDNA allows non-invasive tumor profiling. Liquid biopsy studies with clinical correlation have so far been mainly limited to small size cohorts. Methods: We performed comprehensive plasma genomic testing of ctDNA (NGS) in 670 patients (pts) (54-70 genes); Guardant Health, Inc.; (Clinical Laboratory Improvement Amendment certified and College of American Pathologists accredited). Results: The most represented cancers were gastrointestinal (31.8%), brain (22.7%), and lung (20.7%) (Table). Sixty-three percent of pts (N = 423) had ≥1 alteration. The most frequent alterations (characterized and variants of unknown significance (VUSs)) were in TP53 (32.5% of pts), followed by EGFR (13%), KRAS (12.5%), and PIK3CA (9.1%); for characterized alterations, the breakdown was 30.7% ( TP53), 7.6% ( EGFR), 12.2% ( KRAS), and 7.7% ( PIK3CA). Interestingly, 32% of brain tumors had ≥1 ctDNA alteration. Head and neck tumors were independently associated with a higher number of alterations (P=0.019). Forty-eight percent of pts (320/670) had potentially actionable alterations; in 241, (75% of 320), by an FDA-approved drug (mostly off label). Illustrative examples of clinical utility will be presented such as a patient with gastric cancer and EGFRamplification in ctDNA who received anti-EGFR treatment (60% regression), as well a patient with aggressive gynecologic malignancy who received immunotherapy based on a hypermutated ctDNA profile. Conclusions: Most pts, including a subset of those with brain tumors, demonstrated ctDNA alterations. Pts with head and neck tumors harbored higher numbers of alterations. Overall, three quarters of pts with alteration(s) had ≥1 aberration that could potentially be pharmacologically tractable, suggesting the need to further assess the utility of ctDNA in a therapeutic setting. [Table: see text]

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Next-generation sequencing approach to hyperCKemia

Neurology Genetics ◽

10.1212/nxg.0000000000000352 ◽

2019 ◽

Vol 5 (5) ◽

pp. e352 ◽

Cited By ~ 4

Author(s):

Anna Rubegni ◽

Alessandro Malandrini ◽

Claudia Dosi ◽

Guja Astrea ◽

Jacopo Baldacci ◽

...

Keyword(s):

Next Generation Sequencing ◽

Molecular Diagnosis ◽

Diagnostic Yield ◽

Clinical Neurology ◽

Next Generation ◽

Variants Of Unknown Significance ◽

Unknown Significance ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

ObjectiveNext-generation sequencing (NGS) was applied in molecularly undiagnosed asymptomatic or paucisymptomatic hyperCKemia to investigate whether this technique might allow detection of the genetic basis of the condition.MethodsSixty-six patients with undiagnosed asymptomatic or paucisymptomatic hyperCKemia, referred to tertiary neuromuscular centers over an approximately 2-year period, were analyzed using a customized, targeted sequencing panel able to investigate the coding exons and flanking intronic regions of 78 genes associated with limb-girdle muscular dystrophies, rhabdomyolysis, and metabolic and distal myopathies.ResultsA molecular diagnosis was reached in 33 cases, corresponding to a positive diagnostic yield of 50%. Variants of unknown significance were found in 17 patients (26%), whereas 16 cases (24%) remained molecularly undefined. The major features of the diagnosed cases were mild proximal muscle weakness (found in 27%) and myalgia (in 24%). Fourteen patients with a molecular diagnosis and mild myopathic features on muscle biopsy remained asymptomatic at a 24-month follow-up.ConclusionsThis study of patients with undiagnosed hyperCKemia, highlighting the advantages of NGS used as a first-tier diagnostic approach in genetically heterogeneous conditions, illustrates the ongoing evolution of molecular diagnosis in the field of clinical neurology. Isolated hyperCKemia can be the sole feature alerting to a progressive muscular disorder requiring careful surveillance.

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

Scientific Reports ◽

10.1038/s41598-021-88586-w ◽

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.

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Molecular Autopsy of Sudden Cardiac Death in the Genomics Era

Diagnostics ◽

10.3390/diagnostics11081378 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1378

Author(s):

Vincenzo Castiglione ◽

Martina Modena ◽

Alberto Aimo ◽

Enrica Chiti ◽

Nicoletta Botto ◽

...

Keyword(s):

Diagnostic Features ◽

Molecular Autopsy ◽

Variants Of Unknown Significance ◽

Pathogenic Variants ◽

Genome Wide ◽

Unknown Significance ◽

New Challenges ◽

Next Generation Sequencing Ngs ◽

Cascade Genetic Screening ◽

Generation Sequencing

Molecular autopsy is the process of investigating sudden death through genetic analysis. It is particularly useful in cases where traditional autopsy is negative or only shows non-diagnostic features, i.e., in sudden unexplained deaths (SUDs), which are often due to an underlying inherited arrhythmogenic cardiac disease. The final goal of molecular autopsy in SUD cases is to aid medico-legal inquiries and to guide cascade genetic screening of the victim’s relatives. Early attempts of molecular autopsy relied on Sanger sequencing, which, despite being accurate and easy to use, has a low throughput and can only be employed to analyse a small panel of genes. Conversely, the recent adoption of next-generation sequencing (NGS) technologies has allowed exome/genome wide examination, providing an increase in detection of pathogenic variants and the discovery of newer genotype-phenotype associations. NGS has nonetheless brought new challenges to molecular autopsy, especially regarding the clinical interpretation of the large number of variants of unknown significance detected in each individual.

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Genetic risk assessment for hereditary RCC: Report from the consensus panel meeting.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.6_suppl.615 ◽

2020 ◽

Vol 38 (6_suppl) ◽

pp. 615-615

Author(s):

Michael Daneshvar ◽

Neil Mendhiratta ◽

Ramaprasad Srinivasan ◽

Eric Jonasch ◽

Mark Wayne Ball ◽

...

Keyword(s):

Risk Assessment ◽

Genetic Testing ◽

Kidney Cancer ◽

Genetic Risk ◽

Genetic Counselors ◽

Genetic Risk Assessment ◽

Variants Of Unknown Significance ◽

Modified Delphi ◽

Unknown Significance ◽

Patient Advocates

615 Background: While many genes are now known to be associated with hereditary kidney cancer syndromes, there is a paucity of guidelines or uniform consensus on genetic testing for these patients. An expert panel was organized to assess who, what, when and how patients should be evaluated and what testing should be initiated. Methods: A national, multidisciplinary, panel of experts in urology, medical oncology, clinical geneticists, genetic counselors and patient advocates with background and knowledge in hereditary syndromic kidney cancer convened in person in September 2019. A renal cell carcinoma (RCC) genetic risk assessment questionnaire consisting of 52 questions was compiled prior to the meeting using modified Delphi methodology. The questions were then discussed and reviewed with uniform consensus defined as a minimum of 85% agreement in accordance with the National Comprehensive Cancer Network criteria. Results: The panel consisted of twenty-six attendees represented by urologists (43%), medical oncologist (23%), genetic counselors (13%), clinical geneticists (7%), and patient advocates (3%). The questionnaire consisted of fifty-five statements focusing on who, what, when and how genetic testing should be performed in a patient suspected of hereditary RCC syndrome. A >85% agreement was reached on 30/52 statements with 18/25 (72%) achieving consensus addressing “who”, 2/6 (33%) achieving consensus in “what’ category, 2/7 (29%) in ‘when’ and 4/6 (67%) on how. The questions with least consensus were found in the “what/when?” category with only 4/13 questions with minimum 85% agreement. Specific areas of debate included an age cutoff for prompting a genetic risk assessment as well as need for familial testing in patients with variants of unknown significance. Conclusions: Despite experience of the panel in management of hereditary RCC, the consensus was reached only on 66% of genetic testing. While many issues will need to be discussed further, those statements with consensus may be used to guide physicians and patients on who, what, when and how genetic RCC risk assessment should be performed.

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