A kidney-disease gene panel allows a comprehensive genetic diagnosis of cystic and glomerular inherited kidney diseases
2018; Elsevier BV; Volume: 94; Issue: 2 Linguagem: Inglês
10.1016/j.kint.2018.02.027
ISSN1523-1755
AutoresGemma Bullich, Andrea Domingo-Gallego, Iván Vargas, Patricia Ruíz, Laura Lorente-Grandoso, Mónica Furlano, Gloria Fraga, A. Madrid, Gema Ariceta, Mar Borregán, Juan Alberto Piñero‐Fernández, Lidia Rodríguez-Peña, María Juliana Ballesta‐Martínez, Isabel Llano‐Rivas, Mireia Aguirre Meñica, José Ballarín, David Torrents, Roser Torrá, Elisabet Ars,
Tópico(s)Genetic and Kidney Cyst Diseases
ResumoMolecular diagnosis of inherited kidney diseases remains a challenge due to their expanding phenotypic spectra as well as the constantly growing list of disease-causing genes. Here we develop a comprehensive approach for genetic diagnosis of inherited cystic and glomerular nephropathies. Targeted next generation sequencing of 140 genes causative of or associated with cystic or glomerular nephropathies was performed in 421 patients, a validation cohort of 116 patients with previously known mutations, and a diagnostic cohort of 207 patients with suspected inherited cystic disease and 98 patients with glomerular disease. In the validation cohort, a sensitivity of 99% was achieved. In the diagnostic cohort, causative mutations were found in 78% of patients with cystic disease and 62% of patients with glomerular disease, mostly familial cases, including copy number variants. Results depict the distribution of different cystic and glomerular inherited diseases showing the most likely diagnosis according to perinatal, pediatric and adult disease onset. Of all the genetically diagnosed patients, 15% were referred with an unspecified clinical diagnosis and in 2% genetic testing changed the clinical diagnosis. Therefore, in 17% of cases our genetic analysis was crucial to establish the correct diagnosis. Complex inheritance patterns in autosomal dominant polycystic kidney disease and Alport syndrome were suspected in seven and six patients, respectively. Thus, our kidney-disease gene panel is a comprehensive, noninvasive, and cost-effective tool for genetic diagnosis of cystic and glomerular inherited kidney diseases. This allows etiologic diagnosis in three-quarters of patients and is especially valuable in patients with unspecific or atypical phenotypes. Molecular diagnosis of inherited kidney diseases remains a challenge due to their expanding phenotypic spectra as well as the constantly growing list of disease-causing genes. Here we develop a comprehensive approach for genetic diagnosis of inherited cystic and glomerular nephropathies. Targeted next generation sequencing of 140 genes causative of or associated with cystic or glomerular nephropathies was performed in 421 patients, a validation cohort of 116 patients with previously known mutations, and a diagnostic cohort of 207 patients with suspected inherited cystic disease and 98 patients with glomerular disease. In the validation cohort, a sensitivity of 99% was achieved. In the diagnostic cohort, causative mutations were found in 78% of patients with cystic disease and 62% of patients with glomerular disease, mostly familial cases, including copy number variants. Results depict the distribution of different cystic and glomerular inherited diseases showing the most likely diagnosis according to perinatal, pediatric and adult disease onset. Of all the genetically diagnosed patients, 15% were referred with an unspecified clinical diagnosis and in 2% genetic testing changed the clinical diagnosis. Therefore, in 17% of cases our genetic analysis was crucial to establish the correct diagnosis. Complex inheritance patterns in autosomal dominant polycystic kidney disease and Alport syndrome were suspected in seven and six patients, respectively. Thus, our kidney-disease gene panel is a comprehensive, noninvasive, and cost-effective tool for genetic diagnosis of cystic and glomerular inherited kidney diseases. This allows etiologic diagnosis in three-quarters of patients and is especially valuable in patients with unspecific or atypical phenotypes. Inherited kidney diseases (IKDs) are the leading cause of chronic kidney disease (CKD) in children and account for at least 10% of cases of end-stage renal disease (ESRD) in Europe.1ERA-EDTA Registry: ERA-EDTA Registry Annual Report 2009. Academic Medical Center, Department of Medical Informatics, Amsterdam, The Netherlands2011Google Scholar The most common IKDs are cystic and glomerular nephropathies.2Alkanderi S. Yates L.M. Johnson S.A. Sayer J.A. Lessons learned from a multidisciplinary renal genetics clinic.QJM. 2017; 110: 453-457Crossref PubMed Scopus (21) Google Scholar, 3Mallett A. Fowles L.F. McGaughran J. et al.A multidisciplinary renal genetics clinic improves patient diagnosis.Med J Aust. 2016; 204: 58-59Crossref PubMed Scopus (18) Google Scholar Cystic IKDs encompass different diseases and syndromes characterized by the formation of renal cysts that disrupt the structure of the nephron. To date, about 100 genes causing cystic IKDs have been described; most are expressed in the primary cilium of renal tubular cells, so these diseases are globally called ciliopathies.4Vivante A. Hildebrandt F. Exploring the genetic basis of early-onset chronic kidney disease.Nat Rev Nephrol. 2016; 12: 133-146Crossref PubMed Scopus (198) Google Scholar Cystic IKDs manifest with a broad range of phenotypes ranging from adult-onset mild disease to perinatal lethal disease. Autosomal dominant polycystic kidney disease (ADPKD) is the most common IKD. It is typically an adult-onset disease caused by mutations in PKD1 or PKD2. Autosomal recessive polycystic kidney disease (ARPKD) generally presents in the perinatal period and is caused by mutations in the PKHD1 gene. About 2% to 5% of ADPKD patients show an early and severe phenotype clinically indistinguishable from ARPKD.5Bergmann C. ARPKD and early manifestations of ADPKD: the original polycystic kidney disease and phenocopies.Pediatr Nephrol. 2015; 30: 15-30Crossref PubMed Scopus (103) Google Scholar Some of these severely affected patients carry >1 mutation in cystic IKD genes, probably aggravating the phenotype.6Bergmann C. von Bothmer J. Ortiz Brüchle N. et al.Mutations in multiple PKD genes may explain early and severe polycystic kidney disease.J Am Soc Nephrol. 2011; 22: 2047-2056Crossref PubMed Scopus (171) Google Scholar Clinical manifestations of cystic IKD can be mimicked by mutations in HNF1B, which can cause a spectrum of related diseases (HNF1B-RDs), as well as by mutations in genes that typically cause nephronophthisis-related ciliopathies (NPHP-RCs), especially in the perinatal period and early childhood.5Bergmann C. ARPKD and early manifestations of ADPKD: the original polycystic kidney disease and phenocopies.Pediatr Nephrol. 2015; 30: 15-30Crossref PubMed Scopus (103) Google Scholar NPHP-RCs include a broad range of pediatric AR diseases with high genetic heterogeneity.4Vivante A. Hildebrandt F. Exploring the genetic basis of early-onset chronic kidney disease.Nat Rev Nephrol. 2016; 12: 133-146Crossref PubMed Scopus (198) Google Scholar Renal cysts can also be present in several multisystemic diseases such as tuberous sclerosis complex (TSC), autosomal dominant polycystic liver disease, oral-facial-digital syndrome, and renal coloboma syndrome.7Cramer M.T. Guay-Woodford L.M. Cystic kidney disease: a primer.Adv Chronic Kidney Dis. 2015; 22: 297-305Abstract Full Text Full Text PDF PubMed Scopus (24) Google Scholar Glomerular IKDs manifest with proteinuria or microhematuria or both caused by structural defects in the glomerular basement membrane or the podocytes. Currently, >50 genes responsible for glomerular IKDs have been described.8Bierzynska A. Soderquest K. Dean P. et al.MAGI2 mutations cause congenital nephrotic syndrome.J Am Soc Nephrol. 2017; 28: 1614-1621Crossref PubMed Scopus (45) Google Scholar Alport syndrome (AS) is the most common glomerular IKD and can be caused by mutations in the COL4A5 (X-linked AS), COL4A3, or COL4A4 genes (ARAS or autosomal dominant AS [ADAS]).9Kruegel J. Rubel D. Gross O. Alport syndrome—insights from basic and clinical research.Nat Rev Nephrol. 2013; 9: 170-178Crossref PubMed Scopus (171) Google Scholar Phenotypic overlap with AS can be found in MYH9-RD and COL4A1-RD.10Savoia A. Pecci A. MYH9-related disorders.in: Adam M.P. Ardinger H.H. Pagon R.A. GeneReviews. University of Washington, Seattle, WA2008: 1993-2018Google Scholar, 11Plaisier E. Ronco P. COL4A1-related disorders.in: Adam M.P. Ardinger H.H. Pagon R.A. GeneReviews. University of Washington, Seattle, WA2009: 1993-2018Google Scholar Steroid-resistant nephrotic syndrome (SRNS) has a high genetic heterogeneity, with >40 causative genes described to date. The genetic diagnostic performance is inversely correlated with age of onset, ranging from almost 100% of patients with congenital NS to around 30% of families manifesting before 25 years of age and much lower in sporadic cases. NPHS2, NPHS1, and WT1 are the most frequently mutated genes.12Santín S. Bullich G. Tazón-Vega B. et al.Clinical utility of genetic testing in children and adults with steroid-resistant nephrotic syndrome.Clin J Am Soc Nephrol. 2011; 6: 1139-1148Crossref PubMed Scopus (174) Google Scholar, 13Sadowski C.E. Lovric S. Ashraf S. et al.A single-gene cause in 29.5% of cases of steroid-resistant nephrotic syndrome.J Am Soc Nephrol. 2015; 26: 1279-1289Crossref PubMed Scopus (393) Google Scholar Focal segmental glomerulosclerosis (FSGS) represents the most common biopsy finding in pediatric patients with SRNS.14Trautmann A. Bodria M. Ozaltin F. et al.Spectrum of steroid-resistant and congenital nephrotic syndrome in children: the podoNet registry cohort.Clin J Am Soc Nephrol. 2015; 10: 592-600Crossref PubMed Scopus (191) Google Scholar Adult familial FSGS has been found to be mostly caused by mutations in COL4A3, COL4A4, NPHS2 (p.R229Q variant in trans with a pathogenic mutation), INF2, and TRPC6.12Santín S. Bullich G. Tazón-Vega B. et al.Clinical utility of genetic testing in children and adults with steroid-resistant nephrotic syndrome.Clin J Am Soc Nephrol. 2011; 6: 1139-1148Crossref PubMed Scopus (174) Google Scholar, 15Malone A.F. Phelan P.J. Hall G. et al.Rare hereditary COL4A3/COL4A4 variants may be mistaken for familial focal segmental glomerulosclerosis.Kidney Int. 2014; 86: 1253-1259Abstract Full Text Full Text PDF PubMed Scopus (155) Google Scholar, 16Gast C. Pengelly R.J. Lyon M. et al.Collagen (COL4A) mutations are the most frequent mutations underlying adult focal segmental glomerulosclerosis.Nephrol Dial Transplant. 2016; 31: 961-970Crossref PubMed Scopus (149) Google Scholar In this study, we used a genetic diagnosis approach based on targeted next-generation sequencing of 140 genes causative of cystic and glomerular IKDs in a total of 421 patients, including a validation cohort (n = 116) with previously known mutations and a diagnostic cohort (n = 305) with suspected inherited cystic (n = 207) and glomerular (n = 98) diseases. We aimed to (i) develop a global tool for comprehensive and efficient diagnosis of cystic and glomerular IKDs that is able to identify all types of genetic variants; (ii) determine the distribution of the different inherited cystic and glomerular diseases within our cohort depending on the age at disease onset; (iii) elucidate the genetic cause of disease in patients with atypical phenotypes. Mutations were identified in 115 of the 116 patients in the validation cohort. A total of 134 of the 135 previously known mutations were detected in their correct heterozygous or homozygous state, for a sensitivity of 99%. The detected mutations included 76 single nucleotide variants (SNVs), 26 small (20 base pairs or less) deletions, 9 small insertions, 4 insertions and deletions, 17 large deletions, and 2 large insertions. The only undetected mutation was a small insertion in PKD1 exon 1. No spurious pathogenic mutations were found in any of these samples. The results of the validation cohort have been partially published for ADPKD and SRNS.17Trujillano D. Bullich G. Ossowski S. et al.Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing.Mol Genet Genomic Med. 2014; 2: 412-421Crossref PubMed Scopus (50) Google Scholar, 18Bullich G. Trujillano D. Santin S. et al.Targeted next-generation sequencing in steroid-resistant nephrotic syndrome: mutations in multiple glomerular genes may influence disease severity.Eur J Hum Genet. 2015; 23: 1192-1199Crossref PubMed Scopus (59) Google Scholar We identified disease-causing mutations in 78% (161 of 207) of patients with suspected cystic IKD (Supplementary Table S1), 44% of whom had a positive family history of cystic IKDs. Comparison between the clinical suspicion and the definitive molecular diagnosis is shown in Figure 1a . The clinical diagnosis was confirmed in 129 patients and changed in 3 patients, and a molecular diagnosis was made in 29 patients referred with an unspecific cystic disease (Figure 1b). The detected mutations included SNVs (n = 131), small deletions (n = 46) and insertions (n = 10), insertions and deletions (n = 1), and large deletions (n =24). We designated as disease-causing mutations those variants predicted to be definitely pathogenic or likely pathogenic, 86 of whom were novel (nontruncating likely pathogenic variants are listed in Supplementary Table S2). All patients with prenatal presentation of a suspected cystic IKD were referred with an unspecified clinical diagnosis, and our genetic analysis allowed the etiologic diagnosis in 81% (25 of 31) of them (Figure 2, Supplementary Table S1). The most prevalent cystic IKD with prenatal presentation was ARPKD (42%, 13 of 31), followed by NPHP-RC (19%, 6 of 31), HNF1B-RD (16%, 5 of 31), and ADPKD (3%, 1 of 31). A genetic cause of the disease was identified in 79% (19 of 24) of fetuses with oligo- or anhydramnios that resulted in a legal termination of pregnancy. These patients carried mutations in PKDH1 (n = 13), NPHP3 (n = 2), TMEM67 (n = 2), NEK8 (n = 1), or HNF1B (n = 1). A disease-causing mutation was identified in 86% (6 of 7) of prenatally diagnosed patients who survived, carrying mutations in HNF1B (n = 4), PKD1 (n = 1), or CEP290 (n = 1). The diagnostic yield in patients with pediatric diagnosis (from birth to 18 years) of cystic IKDs was 72% (46 of 64) (Figure 2, Supplementary Table S1). ARPKD and ADPKD were the most frequent molecular diagnoses (both in 19%, 12 of 64), but their frequency was only slightly higher than that of NPHP-RC (in 16%, 10 of 64), followed by HNF1B-RD (9%, 6 of 64). A genetic cause of the disease was identified in 30% (3 of 10) of pediatric patients referred with an unspecific cystic IKD. Their molecular diagnoses were ARPKD (patient UPKD-014), NPHP-RC (patient UPKD-022), and HNF1B-RD (patient UPKD-028). A change in clinical diagnosis was made in a patient with initial suspicion of NPHP-RC who presented with microcysts and CKD at the age of 17 months. His mother had an unspecified glomerulopathy. At the age of 13 years, the proband presented CKD stage III with proteinuria. Ophthalmological revision was normal. Genetic testing detected a PAX2 mutation (patient PAX2-003). In patients with adult-onset cystic disease, a molecular diagnosis was achieved in 80% of patients (90 of 112) (Figure 2, Supplementary Table S1). The most prevalent cystic IKD was ADPKD, accounting for 67% (75 of 112) of patients. For the unspecified cystic IKD patients, we obtained a molecular diagnosis in 20% (1 of 5), consisting of ARPKD (patient UPKD-015) but with extremely mild clinical presentation. A change in clinical diagnosis was made in 2 patients with initial suspicion of ADPKD. Patient OFD1-001, with oral-facial-digital syndrome, was a 35-year-old woman presenting with ESRD and multiple bilateral renal cysts without extrarenal manifestations who carried an OFD1 mutation. Patient ADPLD-001, with autosomal dominant polycystic liver disease, was a 40-year-old woman with bilateral renal cysts, multiple hepatic cysts, and an intracranial aneurysm, whose mother and maternal aunt presented with multiple hepatic and renal cysts with normal renal function. All 3 affected family members carried a truncating mutation in the PRKCSH gene. Mosaic mutations were identified in 3 patients with TSC. Mutant allele frequency was 14% (246 of 5024 reads) in patient TSC-021, 15% (127 of 722 reads) in patient TSC-032, and 9% (190 of 2109 reads) in patient TSC-040. Complex inheritance patterns in ADPKD genes were suspected in 7 patients. Clinical evidence for a potential contribution of all the variants to the severity of the disease could be assessed in 2 of them. Patient ADPKD-216 reached ESRD at 51 years of age and carried the PKD2 truncating mutation p.(Ser74Profs*43) together with the PKD1 missense variant p.(Glu1811Lys), classified as indeterminate clinical significance in the ADPKD mutation database (http://pkdb.mayo.edu/). Patient ADPKD-184 reached ESRD at 36 years old and carried 2 PKD1 variants in trans, p.(Glu2771Lys) and p.(Arg3348Gln) reported in the ADPKD mutation database as highly likely pathogenic and likely pathogenic, respectively, together with a previously reported likely hypomorphic variant p.(Arg2765Cys) in cis with the p.(Arg3348Gln) variant. The remaining 5 ADPKD patients had an earlier presentation or a more severe phenotype than typical ADPKD or both, but had no available family members to analyze whether the variants were inherited in cis, in trans, or presented a de novo mutation (ADPKD-192, -245, -272, -282, -325). We identified disease-causing mutations in 62% (61 of 98) of patients with suspected glomerular IKDs (Supplementary Table S3), 81% of whom had a positive family history of glomerulopathy. The comparison between the clinical suspicion and the definitive molecular diagnosis is shown in Figure 1a. The clinical suspicion was confirmed in 55 patients and changed in 1 patient, and a diagnosis was made in 5 patients referred with an unspecific glomerulopathy (Figure 1b). The detected mutations included SNVs (n = 61), small deletions (n = 10) and insertions (n = 3), insertions and deletions (n = 1), and large deletions (n = 2) and insertions (n = 2), of whom 43 were novel (nontruncating likely pathogenic variants are listed in Supplementary Table S4). All 5 patients with congenital-onset glomerular IKD (from birth to 3 months) were molecularly confirmed as congenital nephrotic syndrome (Figure 3, Supplementary Table S3). Disease-causing mutations were detected in the NPHS1 (n = 4) and the WT1 (n = 1) genes. Among patients with pediatric onset of the disease (from 4 months to 18 years) a molecular diagnosis was achieved in 52% (26 of 50) (Figure 3, Supplementary Table S3), 77% of whom had a positive family history of glomerulopathy. AS was the most frequent molecular diagnosis, accounting for 38% of patients (19 of 50), one-half of them with X-linked AS (9 of 19). Molecularly confirmed SRNS represented 8% (4 of 50) of patients in this cohort. A high genetic heterogeneity was found in these patients, with mutations not only in the most frequently mutated genes but also in less-studied genes such as CUBN and NUP293. A genetic cause of the glomerular disease was found in 33% (2 of 6) of pediatric patients with an unspecified clinical diagnosis, who carried mutations in LMX1B (patient UGLO-001) and PAX2 (patient UGLO-005). A molecular diagnosis different from the clinical diagnosis was found in patient COL4A1-RD-003 with clinical suspicion of AS due to microhematuria, proteinuria, congenital cataracts, and microcornea but carrying a de novo mutation in COL4A1. Of the 24 pediatric patients with negative genetic testing, 79% (19 of 24) presented with nonfamilial SRNS, 17% (4 of 24) with unspecified glomerulopathy, and 4% (1 of 24) with clinical suspicion of AS. In patients with adult-onset disease, we identified a disease-causing mutation in 70% (30 of 43) of patients (Figure 3, Supplementary Table S3), 93% of whom had a positive family history of glomerulopathy. The most frequent molecular diagnosis was AS, accounting for 61 (26 of 43) of patients, mostly ADAS (19 of 26). Disease-causing mutations were found in 43% (3 of 7) of patients referred with an unspecific glomerular IKD, carrying compound heterozygous NPHS1 mutations (patient UGLO-002) and heterozygous WT1 (UGLO-003) or COL4A4 (UGLO-004) mutations. Digenic inheritance with mutations in 2 COL4A genes was suspected in 6 patients, 2 with a pediatric onset of the disease and 4 with adult-onset disease. Clinical evidence for a potential contribution of both variants to the phenotype was found in patient AS-057, who reached ESRD at 26 years and had bilateral hearing loss. Molecular analysis revealed a nonsense mutation in COL4A5 together with a missense variant in COL4A4 predicted to be highly likely pathogenic. Her sister, who carried only the COL4A4 variant, presented with microhematuria, proteinuria, and bilateral hearing loss at 32 years with normal renal function at 47 years. In contrast, intrafamilial phenotypic variability not attributable to the 2 COL4 variants was found in family AS-252. The proband of this family had CKD stage IV at 54 years, whereas only microhematuria with normal renal function was detected in her 48- and 50-year-old sisters. However, molecular analysis revealed that all of them carried heterozygous COL4A3 (p.T781_G783del) and COL4A4 (p.Arg1682Gln) variants predicted to be likely pathogenic. In the remaining patients (AS-269, AS-277, AS-287, and AS-288), no more family members were available to assess the contribution of both variants to the phenotype. Here, we present our 3-year experience using an extensive 140–kidney disease gene panel for the genetic diagnosis of a Spanish cohort of 421 patients with suspected cystic or glomerular IKDs. Our results depict the distribution of inherited cystic and glomerular diseases according to the age at disease onset and show how genetic testing allows the achievement of a definitive diagnosis that in some patients may even differ from the initial clinical suspicion. Clinicians are being confronted with an expanding phenotypic spectra of IKDs as well as a constantly growing list of disease-causing genes.19Stokman M.F. Renkema K.Y. Giles R.H. et al.The expanding phenotypic spectra of kidney diseases: insights from genetic studies.Nat Rev Nephrol. 2016; 12: 472-483Crossref PubMed Scopus (52) Google Scholar, 20Ars E. Torra R. Rare diseases, rare presentations: recognizing atypical inherited kidney disease phenotypes in the age of genomics.Clin Kidney J. 2017; 10: 586-593Crossref PubMed Scopus (13) Google Scholar Therefore, broader diagnostic approaches are required. Whole exome sequencing has been used as a global diagnostic tool for IKD,21Gee H.Y. Otto E.A. Hurd T.W. et al.Whole-exome resequencing distinguishes cystic kidney diseases from phenocopies in renal ciliopathies.Kidney Int. 2014; 85: 880-887Abstract Full Text Full Text PDF PubMed Scopus (54) Google Scholar but it is not an accurate approach to screen for mutations in the main causative gene of IKDs, PKD1, which has 6 almost identical pseudogenes. PKD1 complexity also explains why it has been excluded from several cystic kidney disease panels. Moreover, some genes such as TTC21B and PAX2, initially involved in cystic IKD, have recently been associated with glomerular IKDs,22Davis E.E. Zhang Q. Liu Q. et al.TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum.Nat Genet. 2011; 43: 189-196Crossref PubMed Scopus (266) Google Scholar, 23Huynh Cong E. Bizet A.A. Boyer O. et al.A homozygous missense mutation in the ciliary gene TTC21B causes familial FSGS.J Am Soc Nephrol. 2014; 25: 2435-2443Crossref PubMed Scopus (72) Google Scholar, 24Sanyanusin P. Schimmenti L.A. McNoe L.A. et al.Mutation of the PAX2 gene in a family with optic nerve colobomas, renal anomalies and vesicoureteral reflux.Nat Genet. 1995; 9: 358-364Crossref PubMed Scopus (576) Google Scholar, 25Barua M. Stellacci E. Stella L. et al.Mutations in PAX2 associate with adult-onset FSGS.J Am Soc Nephrol. 2014; 25: 1942-1953Crossref PubMed Scopus (69) Google Scholar as illustrated by our 2 patients carrying PAX2 mutations, 1 of them with clinical suspicion of NPHP-RC (PAX2-003) and the other with unspecified glomerular IKD (UGLO-005). Because cystic and glomerular nephropathies are the most common IKDs, we have developed a genetic diagnostic approach based on capture enrichment, which has proved suitable for PKD1,17Trujillano D. Bullich G. Ossowski S. et al.Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing.Mol Genet Genomic Med. 2014; 2: 412-421Crossref PubMed Scopus (50) Google Scholar, 26Eisenberger T. Decker C. Hiersche M. et al.An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease.PLoS One. 2015; 10: e0116680Crossref PubMed Scopus (53) Google Scholar to simultaneously sequence 140 genes causative of these diseases. A high sensitivity and specificity for detection of all types of genetic variants, from SNVs to copy number variants (CNVs), was demonstrated in a large validation cohort. In our diagnostic cohort, the genetic cause was identified in 78% of patients with suspected cystic IKDs (44% familial cases) and 62% of patients with suspected glomerular IKDs (81% familial cases). These high diagnostic rates might be explained by our strict inclusion criteria for genetic testing, especially in patients with suspected glomerular IKDs, most of whom had a positive family history. A further plus of our approach is that it allows detection of CNVs, which accounted for 10% of the genetically diagnosed patients (23 of 222), consisting of patients with HNF1B-RD (n = 9), NPHP-RC (n = 5), ADPKD (n = 3), TSC (n = 2), X-linked AS (n = 2), and ADAS (n = 2). Thus, CNVs might account for a nonnegligible proportion of patients with cystic and glomerular IKDs and should be assessed in the routine genetic diagnosis. Recently, a similar approach based on targeted next-generation sequencing of a 127-gene panel was applied to a small cohort of 56 families, achieving a 59% diagnostic yield without detection of any CNV.27Mori T. Hosomichi K. Chiga M. et al.Comprehensive genetic testing approach for major inherited kidney diseases, using next-generation sequencing with a custom panel.Clin Exp Nephrol. 2017; 21: 63-75Crossref PubMed Scopus (32) Google Scholar Another recent study proposed targeted exome sequencing of >2000 Online Mendelian Inheritance in Man (OMIM) disease genes with subsequent phenotype-based analysis limited to 207 renal genes (subdivided into 10 multigene panels) for genetic testing. A genetic diagnosis was identified in 43% of their 135 studied families, consecutively referred to their diagnostic genetic service with no strict inclusion criteria. An advantage of sequencing the broad range of OMIM genes is that additional genes can be further analyzed. However, this approach has several limitations: (i) it does not detect CNVs; (ii) some regions are incompletely covered, requiring Sanger sequencing; and (iii) some complex genes such as PKD1 cannot be evaluated.28Mallett A.J. McCarthy H.J. Ho G. et al.Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders.Kidney Int. 2017; 92: 1493-1506Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar In our cohort, 15% (34 of 222) of all the genetically diagnosed patients were referred with an unspecified clinical diagnosis and 2% (4 of 222) had an inaccurate clinical diagnosis. Therefore, in 17% of cases, our genetic analysis was crucial to establish the correct diagnosis. This is especially relevant in distinguishing between different cystic IKDs in severe fetal cases detected by prenatal ultrasound screening. Some of these patients have a perinatal lethal disease, but the identification of their pathogenic mutations will enable precise genetic counseling of their parents, who may benefit from a future prenatal or preimplantational genetic diagnosis. Our approach allowed a definitive diagnosis in approximately 80% of the patients with a prenatal presentation of cystic IKDs, one-half of them affected by ARPKD. A renal gene panel has been used for the study of a highly consanguineous Saudi Arabian cohort with antenatal cystic IKD. Genetic diagnosis was achieved in 62% to 70% of patients, most of them having NPHP-RC.29Al-Hamed M.H. Kurdi W. Alsahan N. et al.Genetic spectrum of Saudi Arabian patients with antenatal cystic kidney disease and ciliopathy phenotypes using a targeted renal gene panel.J Med Genet. 2016; 53: 338-347Crossref PubMed Scopus (25) Google Scholar Cystic kidneys in children may develop as a result of different diseases and syndromes that vary with regard to their mode of inheritance, age of onset of disease, and severity of renal and extrarenal phenotypes. Clinical approaches based on the kidney size, the localization of cysts, and the presence of extrarenal features have been described.30Kurschat C.E. Muller R.-U. Franke M. et al.An approach to cystic kidney diseases: the clinician’s view.Nat Rev Nephrol. 2014; 10: 687-699Crossref PubMed Scopus (13) Google Scholar However, there is clinical overlap among these diseases that hampers their correct diagnosis. In our patients with pediatric onset of cystic IKDs, the main genetic diagnoses were ARPKD and ADPKD but 16% (10 of 64) were referred with an unspecified clinical diagnosis. The most prevalent cystic IKD in adult-onset patients was ADPKD, accounting for >60% of patients. In this context, it should be borne in mind that genetic diagnosis of ADPKD is only indicated in specific situations.31Ars E. Bernis C. Fraga G. et al.Spanish guidelines for the management of autosomal dominant polycystic kidney disease.Nephrol Dial Transplant. 2014; 29: iv95-iv105Crossref PubMed Scopus (42) Google Scholar Complex inheritance patterns in ADPKD patients may involve incompletely penetrant or hypomorphic PKD1 alleles that cause mild cystic disease when inherited alone or aggravate the severity of the cystic disease in patients with another mutation inherited in trans.32Rossetti S. Kubly V.J. Consugar M.B. et al.Incompletely pe
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