Somatic mosaicism and variant frequency detected by next-generation sequencing in X-linked Alport syndrome

Abstract

X-linked Alport syndrome (XLAS) is a progressive, hereditary nephropathy. Although men with XLAS usually develop end-stage renal disease before 30 years of age, some men show a milder phenotype and develop end-stage renal disease later in life. However, the molecular mechanisms associated with this milder phenotype have not been fully identified. We genetically diagnosed 186 patients with suspected XLAS between January 2006 and August 2014. Genetic examination involved: (1) extraction and analysis of genomic DNA using PCR and direct sequencing using Sanger's method and (2) next-generation sequencing to detect variant allele frequencies. We identified somatic mosaic variants in the type VI collagen, α5 gene (COL4A5) in four patients. Interestingly, two of these four patients with variant frequencies in kidney biopsies or urinary sediment cells of ≥ 50% showed hematuria and moderate proteinuria, whereas the other two with variant frequencies of o50% were asymptomatic or only had hematuria. De novo variants can occur even in asymptomatic male cases of XLAS resulting in mosaicism, with important implications for genetic counseling. This is the first study to show a tendency between the variant allele frequency and disease severity in male XLAS patients with somatic mosaic variants in COL4A5. Although this is a very rare status of somatic mosaicism, further analysis is needed to show this correlation in a larger population.

Expert consensus guidelines for the genetic diagnosis of Alport syndrome

“…Mosaicism can also be demonstrated in males with X-linked Alport syndrome by skin or renal immunohistochemistry. The diagnosis of mosaicism has important consequences for patient management and genetic counselling [59,60].…”

“…A heterozygous variant is unlikely to produce a lamellated GBM and renal failure but combinations of variants in COL4A3 and COL4A4 and in other podocyte-derived genes may do so. When a heterozygous variant is identified, the clinical characteristics range from haematuria to end-stage renal failure [60]. Some heterozygous variants may be associated with extra-renal features [66,67], and treatment with ACE inhibitors also delays the onset of end-stage renal disease [68].…”

Genomic mosaicism in paternal sperm and multiple parental tissues in a Dravet syndrome cohort

“…Sporadic cases of parental pathogenic mosaic mutations have been documented in more than 100 Mendelian disorders 1 – 5 , such as Charcot-Marie-Tooth disease 6 , Dravet syndrome 7 , Freeman-Sheldon syndrome 8 , and epilepsy in females with mental retardation 9 . Parental germline mosaicism and somatic mosaicism in patients have been studied in families affected by Alport syndrome 10 , focal cortical dysplasia type II 11 , extracranial arteriovenous malformation 12 , and epilepsy-related neurodevelopmental disorders 13 at the cohort level. Parental mosaicism has also been reported in cohorts of complex neurological and psychiatric disorders, such as autism spectrum disorder 14 – 17 , intellectual disability 18 , and epileptic encephalopathies 19 .…”

“…However, the differences in mutation frequencies of postzygotic single nucleotide mosaicism are not yet well understood in the context of multiple tissues or in sperm cells at the cohort level for neurological disorders. The existing studies using multiple samples for disorders caused by cancer genes, such as COLA5 10 , MAP2K1 12 , and ASXL1 36 were limited by the detection methods because next-generation sequencing (NGS) approaches and traditional digital PCR based methods have a detection and quantification limit of 0.5–1%. Studies using multiple samples for disorders caused by non-cancer genes, such as ATP1A3 35 , MEFV 38 , PCDH19 39 , 40 , SCN1A 21 , and SCN5A 42 , were limited by their sample sizes, because the collection of a large cohort is difficult and reports tend to appear as case studies.…”

Mosaicism in Traditional Mendelian Diseases

“…Mosaicism has also been described in disorders related to developmental delay and/ or epilepsy syndromes such as Pitt-Hopkins syndrome (caused by mutations in TCF4) [52], Rett syndrome (caused by mutations in MeCP2) [53], Cornelia de Lange syndrome (caused by mutations in NIPBL, SMC1A, SMC3) [54,55], X-linked Charcot-Marie-Tooth type 1 (caused by mutations in GJB1) [56], FOXG1 syndrome [57], benign familial neonatal seizures (KCNQ2) [58], and Temple-Baraitser syndrome (KCNH1) [59]. More recently, mosaicism has been described in X-linked Alport syndrome(COL4A5) [60], a form of nephropathy, …”