SVRare: discovering disease-causing structural variants in the 100K Genomes Project

Discovery of disease-causing structural variants (dcSV) from whole genome sequencing data is difficult due to high number of false positives and a lack of efficient way to estimate allele frequency. Here we introduce SVRare, an application that aggregates structural variants (SV) called by other tools, and efficiently annotates rare SVs to aid dcSVs discovery. Applied in the Genomics England (GEL) research environment to data from the 100K Genomes Project, SVRare aggregated 554,060,126 SVs called by Manta and Canvas in all the 71,408 participants in the rare-disease arm. From a pilot study of 4313 families, SVRare identified 36 novel protein-coding disrupting SVs on diagnostic grade genes that may explain proband's phenotype. It is estimated that SVRare can increase SV-based diagnosis yield by at least 4-fold. We also performed a genome-wide association study, and uncovered clusters of dcSVs in genes with known pathogenicity, such as PKD1/2 - cystic kidney diseases and LDLR - familial hypercholesterolaemia.

Spectrum of Mutations in Pediatric Non-glomerular Chronic Kidney Disease Stages 2–5

Renal hypodysplasia and cystic kidney diseases, the common non-glomerular causes of pediatric chronic kidney disease (CKD), are usually diagnosed by their clinical and imaging characteristics. The high degree of phenotypic heterogeneity, in both conditions, makes the correct final diagnosis dependent on genetic testing. It is not clear, however, whether the frequencies of damaged alleles vary among different ethnicities in children with non-glomerular CKD, and this will influence the strategy used for genetic testing. In this study, 69 unrelated children (40 boys, 29 girls) of predominantly Han Chinese ethnicity with stage 2–5 non-glomerular CKD caused by suspected renal hypodysplasia or cystic kidney diseases were enrolled and assessed by molecular analysis using proband-only targeted exome sequencing and array-comparative genomic hybridization. Targeted exome sequencing discovered genetic etiologies in 33 patients (47.8%) covering 10 distinct genetic disorders. The clinical diagnoses in 13/48 patients (27.1%) with suspected renal hypodysplasia were confirmed, and two patients were reclassified carrying mutations in nephronophthisis (NPHP) genes. The clinical diagnoses in 16/20 patients (80%) with suspected cystic kidney diseases were confirmed, and one patient was reclassified as carrying a deletion in the hepatocyte nuclear factor-1-beta gene (HNF1B). The diagnosis of one patient with unknown non-glomerular disease was elucidated. No copy number variations were identified in the 20 patients with negative targeted exome sequencing results. NPHP genes were the most common disease-causing genes in the patients with disease onsets above 6 years of age (14/45, 31.1%). The children with stage 2 and 3 CKD at onset were found to carry causative mutations in paired box gene 2 (PAX2) and HNF1B gene (11/24, 45.8%), whereas those with stage 4 and 5 CKD mostly carried causative mutations in NPHP genes (19/45, 42.2%). The causative genes were not suspected by the kidney imaging patterns at disease onset. Thus, our data show that in Chinese children with non-glomerular renal dysfunction caused by renal hypodysplasia and cystic kidney diseases, the common causative genes vary with age and CKD stage at disease onset. These findings have the potential to improve management and genetic counseling of these diseases in clinical practice.

Inherited renal disease

With the advancement in, and increased availability of, genetic testing and a rapidly growing understanding of the genetic basis of many kidney diseases, it is important that nephrologists understand the rationale, limitations, and implications of making a genetic diagnosis in patients with kidney disease. While most inherited kidney diseases are rare, all nephrologists will encounter patients with genetic forms of kidney disease, particularly the cystic kidney diseases. An understanding of the genotype–phenotype relationships across the different inherited kidney diseases provides the nephrologist with an unprecedented understanding of disease pathogenesis. The evolving use of gene-based and molecular therapies utilizing silencing RNA molecules in kidney diseases are likely to become a growing therapeutic option in the future. Nephrologists will need to understand and embrace these new therapies, particularly for this group of kidney diseases.

MO045THE APPLICATION OF A NGS KIDNEY PANEL REVEALED KEY CHALLENGES OF PKD1-2 ANALYSIS: INTERPRETATION OF MISSENSE VARIANTS, SIGNIFICANCE OF VARIANTS IN DUPLICATED REGIONS AND HIGH ALLELIC HETEROGENEITY

Background and Aims Genetic testing has changed the clinical management of inherited kidney diseases patients, improving prognosis, surveillance and therapy. On the other hand, it has put geneticists and clinicians in front of new challenges, as the heterogeneity of these disorders and the high number of variants, with no clear genotype-phenotype correlation. Method 108 patients underwent genetic analysis through a kidney focused NGS panel, named Nephroplex, containing 119 genetic loci associated with inherited kidney disorders. The study aimed to addressed the genetic landscape of cystic individuals and to analyze PKD1 and PKD2 variants in non-cystic individuals. Results Following diagnostic criteria, patients were divided as cystic kidney diseases (n=36) and non-cystic kidney diseases (n=72). Among the group of cystic patients, a causative mutation was detected in 51% of cases. We found thirty-seven PKD1 and PKD2 variants in 26 out of 35 individuals. In particular, 12 variants were shown to be damaging and nine of that were reported in public database, as CLINVAR and Mayo Clinic databases. Among pathogenic variants, twelve were truncating and the remaining were missense variants. Of note, 7 out of 12 damaging PKD1 mutations were located in duplicated regions. Moreover, in three cystic patients, we found a (i) a frameshift hemizygote OFD1 mutation (ii) compound heterozygote PKHD1 variants and (iii) a frameshift MUC1 variant, framing the diagnosis of oro-facio-digital type 1, autosomal recessive polycystic kidney disease and autosomal dominant tubulointerstitial disease, respectively. Interestingly, we detected 28 PKD1-2 rare variants in 21 out of 75 adult non cystic patients (28%). The most were observed in PKD1 genes (82% vs 18% in PKD2). Eighteen of 28 variants were described in the literature as likely benign or as mutations of uncertain significance, while we found 10 novel variants. In silico analysis revealed as pathogenic a frameshift mutation located in exon 15. Of note, the great part of these variations reside into the duplicated PKD1 regions. Conclusion Our data showed that genetic analysis of ADPKD retains unique challenges, given the high degree of homology of PKD1 with his pseudogenes and the high allelic heterogeneity in non-cystic individuals.

MO026CLINICAL AND MUTATIONAL SPECTRUM OF CHILDREN WITH AUTOSOMAL RECESSIVE AND AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE

Background and Aims Cystic kidney diseases are a heterogeneous group of chronic renal disease. Autosomal recessive polycystic kidney disease (ARPKD) is generally diagnosed in utero or at birth due to mutations in PKHD1 gene. Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease commonly associated with mutations in PKD1 or PKD2. In this study, we aimed to investigate clinical and genetic features of ARPKD and ADPKD in a group of Turkish patients. Method A total of 69 children with genetically confirmed ARPKD (10 females, 11 males) or ADPKD (28 females, 20 males) from seven pediatric nephrology centers were included in this study. Demographic features, family history, clinical and laboratory findings at presentation and during 12 months intervals were collected. Results For ARPKD patients, the median age at diagnosis was 10.5 (IQR; 0.75-58.5) months. Consanguinity between parents was present in 11 patients (52.4%). At the time of diagnosis, 14 (66.7%) patients had eGFR<90 ml/min/1.73 m2. Mean duration of follow-up was 4.1±3,7 years. At the last visit, median eGFR was 74 (IQR; 43-126) ml/min/1.73m2. A total of 6 patients (28,6%) underwent a renal replacement therapy (RRT), 3 of them died in infancy and 2 of them had renal transplantation during follow up. All patients had bi-allelic PKHD1 mutation. For ADPKD patients, the mean age at diagnosis was 5.5±4.6 years. At the time of diagnosis 11 (22.9%) patients had eGFR<90 ml/min/1.73m2. Mean duration of follow-up was 2,7±2.3 years. At the last visit, median eGFR was 114 (IQR; 98-135) ml/min/1.73m2. Only one patient underwent a renal transplantation. A total of 42 patients (87.5%) had a heterozygous PKD1 mutation while 6 (12.5%) had a heterozygous PKD2 mutation. The rate of growth retardation, hypertension at diagnosis and progression to chronic kidney disease (CKD) were higher in patients with PKHD1 mutation than the patients with PKD1 or PKD2 mutation (p < 0.001, p < 0.001 and p = 0.001, respectively). In kidney survival analysis, mutation type, growth retardation at presentation, increased renal echogenity in ultrasonography were found as independent risk factors for progression to CKD. Conclusion Cystic kidney diseases are one of the most clinically and genetically heterogenous diseases. Differentiating them and establishing the predictors for CKD development is important to provide appropriate management including choosing appropriate donor in renal transplantation.

Autosomal Dominant Polycystic Kidney Disease does not significantly alter major COVID-19 outcomes among veterans

Chronic kidney disease (CKD), as well as its common causes (e.g., diabetes and obesity), are recognized risk factors for severe COVID-19 illness. To explore whether the most common inherited cause of CKD, autosomal dominant polycystic kidney disease (ADPKD), is also an independent risk factor, we studied data from the VA health system and the VA COVID-19-shared resources (e.g., ICD codes, demographics, pre-existing conditions, pre-testing symptoms, and post-testing outcomes). Among 61 COVID-19-positive ADPKD patients, 21 (34.4%) were hospitalized, 10 (16.4%) were admitted to ICU, 4 (6.6%) required ventilator, and 4 (6.6%) died by August 18, 2020. These rates were comparable to patients with other cystic kidney diseases and cystic liver-only diseases. ADPKD was not a significant risk factor for any of the four outcomes in multivariable logistic regression analyses when compared with other cystic kidney diseases and cystic liver-only diseases. In contrast, diabetes was a significant risk factor for hospitalization [OR 2.30 (1.61, 3.30), p<0.001], ICU admission [OR 2.23 (1.47, 3.42), p<0.001], and ventilator requirement [OR 2.20 (1.27, 3.88), p=0.005]. Black race significantly increased the risk for ventilator requirement [OR 2.00 (1.18, 3.44), p=0.011] and mortality [OR 1.60 (1.02, 2.51), p=0.040]. We also examined the outcome of starting dialysis after COVID-19 confirmation. The main risk factor for starting dialysis was CKD [OR 6.37 (2.43, 16.7)] and Black race [OR 3.47 (1.48, 8.1)]. After controlling for CKD, ADPKD did not significantly increase the risk for newly starting dialysis comparing with other cystic kidney diseases and cystic liver-only diseases. In summary, ADPKD did not significantly alter major COVID-19 outcomes among veterans when compared to other cystic kidney and liver patients.

Systematic evaluation of olfaction in patients with hereditary cystic kidney diseases/renal ciliopathies

BackgroundHereditary cystic kidney diseases such as nephronophthisis, polycystic kidney disease and Bardet-Biedl syndrome (BBS) are caused by a dysfunction of primary cilia. Cilia are involved in a variety of cellular functions and perceptions, with one of them being the sense of smell. Hyposmia is a typical feature found in patients with BBS. However, reports of olfactory dysfunction in other cystic kidney diseases are sparse. Here we provide a systematic survey on olfaction in a large cohort of patients displaying genetically determined renal ciliopathies.MethodsWe performed a match-controlled systematic olfactory evaluation in a group of 75 patients with a defined genetic background using age adapted and validated odour identification tests.ResultsTest results revealed a significant olfactory deficit in patients carrying TMEM67 variants (n=4), while all other genetic disorders causing nephronophthisis (n=25) or polycystic kidney disease (n=18) were not associated with an impaired sense of smell. Also in patients with BBS, olfactory performance was depending on the underlying molecular defect. While defects in the BBS1 gene (n=9) had no impact on the sense of smell, all other BBS gene disorders (n=19) were associated with significant hyposmia. Noteworthy, there was no correlation of the olfactory deficit with the level of renal impairment.ConclusionHyposmia is a part of the clinical spectrum of BBS and of other renal ciliopathies. Depending on the genetic background, clinicians should be aware of this subtle and so far underappreciated symptom when clinically assessing patients with BBS or TMEM67 gene variants.