Whole-Exome Sequencing Identifies Causative Mutations in Families with Congenital Anomalies of the Kidney and Urinary Tract

Abstract

Background: Congenital anomalies of the kidney and urinary tract (CAKUT) are the most prevalent cause of kidney disease in the first three decades of life. Previous gene panel studies showed monogenic causation in up to 12% of patients with CAKUT.

Methods: We applied whole-exome sequencing to analyze the genotypes of individuals from 232 families with CAKUT, evaluating for mutations in single genes known to cause human CAKUT and genes known to cause CAKUT in mice. In consanguineous or multiplex families, we additionally performed a search for novel monogenic causes of CAKUT.

Results: In 29 families (13%), we detected a causative mutation in a known gene for isolated or syndromic CAKUT that sufficiently explained the patient's CAKUT phenotype. In three families (1%), we detected a mutation in a gene reported to cause a phenocopy of CAKUT. In 15 of 155 families with isolated CAKUT, we detected deleterious mutations in syndromic CAKUT genes. Our additional search for novel monogenic causes of CAKUT in consanguineous and multiplex families revealed a potential single, novel monogenic CAKUT gene in 19 of 232 families (8%).

Conclusions: We identified monogenic mutations in a known human CAKUT gene or CAKUT phenocopy gene as the cause of disease in 14% of the CAKUT families in this study. Whole-exome sequencing provides an etiologic diagnosis in a high fraction of patients with CAKUT and will provide a new basis for the mechanistic understanding of CAKUT.

Keywords: Congenital Anomalies of the Kidney and Urinary Tract (CAKUT); Vesico-ureteral Reflux (VUR); Whole Exome Sequencing (WES); monogenic disease causation; renal developmental gene.

Figure 1.

Number and percentage of 232 congenital anomalies of the kidney and urinary tract (CAKUT) families in which a causative mutation in a known monogenic CAKUT gene (14%) or a candidate gene(s) (16%) was detected by whole-exome sequencing. Blue color denotes that a mutation in a single causative gene was detected in a known isolated or syndromic CAKUT gene (dark blue), and purple color denotes that a mutation in a causative gene was known to phenocopy CAKUT (purple). Light blue denotes candidate mutations in a known syndromic CAKUT gene in families with isolated CAKUT (light blue). Pink was chosen if a candidate variant in a murine CAKUT gene was identified. Red was chosen if one potential novel CAKUT gene was detected in a family, or green was chosen if multiple novel candidate genes for CAKUT were detected in a family. (A) In 29 of 232 (13%) families with CAKUT (dark blue), a causative mutation was detected in one of 40 isolated CAKUT genes (Supplemental Table 1) or one of 179 known syndromic CAKUT genes (Supplemental Table 2). The individuals with mutations in a syndromic CAKUT gene exhibited the corresponding syndromic CAKUT phenotype. (B) In three of 232 (1%) families, a mutation was identified in a gene causing a kidney disease that may represent a phenocopy of CAKUT (purple; i.e., small kidneys of non-CAKUT origin). (C) In 15 of 232 (6%) families with predominantly isolated CAKUT, candidate mutations were detected in one of 179 syndromic CAKUT genes (light blue), indicating a “hypomorphic” effect of these mutations. (D) In five of 232 (2%) families, mutations in a known gene for murine CAKUT were identified (pink). (E) In 19 of 232 (8%) families, a single potential novel candidate gene for CAKUT was identified per family (red). (F) In 22 of 232 (9%) families, multiple potential novel candidate genes remained per family (green). (G) In ten of 232 (4%) families, we identified mutations in genes known to be causative of monogenic non-CAKUT diseases (brown). (H) In 129 of 232 (56%) families, no causative or candidate mutations were detected (yellow).

Figure 2.

Inclusion criteria for 232 families to perform whole-exome sequencing (WES). (A) Individuals with congenital anomalies of the kidney and urinary tract (CAKUT) were prioritized for inclusion in WES on the basis of the following criteria: (1) reportedly consanguineous (50 of 232; 22%); (2) reportedly nonconsanguineous but origin in countries with increased rate of consanguinity and therefore, considered likely consanguineous (43 of 232; 18%); (3) syndromic CAKUT phenotype (16 of 232; 7%); (4) severe manifestation of CAKUT (renal agenesis or renal dysplasia; six of 232; 3%); (5) families with multiple affected family members (40 of 232; 17%); (6) DNA of additional family members available for a duo, trio, or quad analysis (60 of 232; 26%); and (7) other reasons to include in WES (e.g., family potentially related to a family to which the other criteria applied; 17 of 232; 7%). Outcome of WES analysis by “recruitment group.” (B) The seven recruitment groups for inclusion in CAKUT WES are sorted horizontally starting with the group with the lowest percentage of unsolved families and going to the group with the highest percentage unsolved. Each group is further subsorted into categories of identified genes. Categories are similar to those in Figure 1, and the colors used are the same as well: (1) solved for isolated or syndromic CAKUT gene (dark blue), (2) phenocopy gene (purple), (3) syndromic gene identified in patients with isolated CAKUT (light blue), (4) mouse CAKUT gene identified (pink), (5) single novel candidate gene identified (red), (6) multiple candidate genes identified (green), (7) non-CAKUT gene identified (brown), and (8) unsolved (yellow).

Figure 3.

Relationship between measured homozygosity and disease-causing mutations in congenital anomalies of the kidney and urinary tract (CAKUT). Homozygosity mapping was performed on the basis of single-nucleotide polymorphisms generated from whole-exome sequencing data. Data are shown for families in which a CAKUT-causing gene or a gene known to phenocopy CAKUT was identified (32 of 232) and families with isolated CAKUT in which a candidate gene in a known syndromic CAKUT gene was identified (15 of 232). A representative individual from each family was plotted from the highest to the lowest level of total homozygosity (megabase pairs) across the genome. In total, seven individuals had homozygosity ≥100 Mbp, whereas 38 individuals had homozygosity of <100 Mbp, which is denoted by the gray dashed line. In two families, homozygosity mapping could not be generated due to low coverage, and therefore, they are not included in this graph (A3887: TBX18 dominant heterozygous mutation and A2962: NPHP1 homozygous variant). Causative mutations in isolated/syndromic genes identified in CAKUT families with the corresponding phenotype are denoted by a dark blue color, phenocopy genes are denoted by a purple color, and candidate mutations in syndromic CAKUT genes identified in families with isolated CAKUT are denoted by a light blue color. Homozygous variants are denoted by filled circles, compound heterozygous variants are denoted by two half circles, dominant heterozygous variants are denoted by unfilled circles, X-linked variants are denoted by an “X,” and complex chromosomal rearrangements are denoted by a “T.” Note that, in the part of our cohort with homozygosity of ≥100 Mbp (the cluster left of the x axis), paradoxically, we identified causative mutations in heterozygous genes (e.g., B1439; SALL1). In patients with rare cases with extreme homozygosity, heterozygous disease-causing mutations can be identified. Such patients have previously been described in the literature.