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      Genetics of Congenital Anomalies of the Kidney and Urinary Tract: The Current State of Play

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          Abstract

          Congenital anomalies of the kidney and urinary tract (CAKUT) are the most frequent form of malformation at birth and represent the cause of 40–50% of pediatric and 7% of adult end-stage renal disease worldwide. The pathogenesis of CAKUT is based on the disturbance of normal nephrogenesis, secondary to environmental and genetic causes. Often CAKUT is the first clinical manifestation of a complex systemic disease, so an early molecular diagnosis can help the physician identify other subtle clinical manifestations, significantly affecting the management and prognosis of patients. The number of sporadic CAKUT cases explained by highly penetrant mutations in a single gene may have been overestimated over the years and a genetic diagnosis is missed in most cases, hence the importance of identifying new genetic approaches which can help unraveling the vast majority of unexplained CAKUT cases. The aim of our review is to clarify the current state of play and the future perspectives of the genetic bases of CAKUT.

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          Global variation in copy number in the human genome.

          Richard Redon, Shumpei Ishikawa, Karen R Fitch … (2006)
          Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
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            Large recurrent microdeletions associated with schizophrenia.

            Hreinn Stefansson, Dan Rujescu, Sven Cichon … (2008)
            Reduced fecundity, associated with severe mental disorders, places negative selection pressure on risk alleles and may explain, in part, why common variants have not been found that confer risk of disorders such as autism, schizophrenia and mental retardation. Thus, rare variants may account for a larger fraction of the overall genetic risk than previously assumed. In contrast to rare single nucleotide mutations, rare copy number variations (CNVs) can be detected using genome-wide single nucleotide polymorphism arrays. This has led to the identification of CNVs associated with mental retardation and autism. In a genome-wide search for CNVs associating with schizophrenia, we used a population-based sample to identify de novo CNVs by analysing 9,878 transmissions from parents to offspring. The 66 de novo CNVs identified were tested for association in a sample of 1,433 schizophrenia cases and 33,250 controls. Three deletions at 1q21.1, 15q11.2 and 15q13.3 showing nominal association with schizophrenia in the first sample (phase I) were followed up in a second sample of 3,285 cases and 7,951 controls (phase II). All three deletions significantly associate with schizophrenia and related psychoses in the combined sample. The identification of these rare, recurrent risk variants, having occurred independently in multiple founders and being subject to negative selection, is important in itself. CNV analysis may also point the way to the identification of additional and more prevalent risk variants in genes and pathways involved in schizophrenia.
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              Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

              Brian O'Roak, Pelagia Deriziotis, Choli Lee … (2011)
              Evidence for the etiology of autism spectrum disorders (ASD) has consistently pointed to a strong genetic component complicated by substantial locus heterogeneity 1,2 . We sequenced the exomes of 20 sporadic cases of ASD and their parents, reasoning that these families would be enriched for de novo mutations of major effect. We identified 21 de novo mutations, of which 11 were protein-altering. Protein-altering mutations were significantly enriched for changes at highly conserved residues. We identified potentially causative de novo events in 4/20 probands, particularly among more severely affected individuals, in FOXP1, GRIN2B, SCN1A, and LAMC3. In the FOXP1 mutation carrier, we also observed a rare inherited CNTNAP2 mutation and provide functional support for a multihit model for disease risk 3 . Our results demonstrate that trio-based exome sequencing is a powerful approach for identifying novel candidate genes for ASD and suggest that de novo mutations may contribute substantially to the genetic risk for ASD.
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                Author and article information

                Contributors
                Alan Parrish: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): Int J Mol Sci
                Journal ID (iso-abbrev): Int J Mol Sci
                Journal ID (publisher-id): ijms
                Title: International Journal of Molecular Sciences
                Publisher: MDPI
                ISSN (Electronic): 1422-0067
                Publication date (Electronic): 11 April 2017
                Publication date Collection: April 2017
                Volume: 18
                Issue: 4
                Electronic Location Identifier: 796
                Affiliations
                Pediatric Nephrology, Dialysis and Transplant Unit, Department of Clinical Sciences and Community Health, University of Milan, Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, 20122 Milano, Italy; valentina.capone@ 123456unimi.it (V.P.C.); williammorello82@ 123456gmail.com (W.M.); francesca.taroni@ 123456policlinico.mi.it (F.T.)
                Author notes
                [* ]Correspondence: giovanni.montini@ 123456unimi.it ; Tel.: +39-02-5503-2336; Fax: +39-02-5503-2451
                Article
                Publisher ID: ijms-18-00796
                DOI: 10.3390/ijms18040796
                PMC ID: 5412380
                PubMed ID: 28398236
                SO-VID: 5bb1d0df-a974-4850-9616-10b82309045e
                Copyright © © 2017 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 23 February 2017
                Date accepted : 07 April 2017
                Categories
                Subject: Review

                ScienceOpen disciplines: Molecular biology
                Keywords: congenital abnormalities of the kidney and urinary tract (cakut),genetics,renal hypodysplasia,next-generation sequencing,copy number variants
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: congenital abnormalities of the kidney and urinary tract (cakut), genetics, renal hypodysplasia, next-generation sequencing, copy number variants

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