Molecular diagnosis of known recessive ataxias by homozygosity mapping with SNP arrays

Abstract

The diagnosis of rare inherited diseases is becoming more and more complex as an increasing number of clinical conditions appear to be genetically heterogeneous. Multigenic inheritance also applies to the autosomal recessive progressive cerebellar ataxias (ARCAs), for which 14 genes have been identified and more are expected to be discovered. We used homozygosity mapping as a guide for identification of the defective locus in patients with ARCA born from consanguineous parents. Patients from 97 families were analyzed with GeneChip Mapping 10K or 50K SNP Affymetrix microarrays. We identified six families homozygous for regions containing the autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) gene, two families homozygous for the ataxia-telangiectasia gene (ATM), two families homozygous for the ataxia with oculomotor apraxia type 1 (AOA1) gene, and one family homozygous for the AOA type 2 (AOA2) gene. Upon direct gene testing, we were able to identify a disease-related mutation in all families but one of the two kindred homozygous at the ATM locus. Although linkage analyses pointed to a single locus on chromosome 11q22.1-q23.1 for this family, clinical features, normal levels of serum alpha-foetoprotein as well as absence of mutations in the ATM gene rather suggest the existence of an additional ARCA-related gene in that interval. While the use of homozygosity mapping was very effective at pointing to the correct gene, it also suggests that the majority of patients harbor mutations either in the genes of the rare forms of ARCA or in genes yet to be identified.

New practical definitions for the diagnosis of autosomal recessive spastic ataxia of Charlevoix–Saguenay

“…According to earlier recommendations on variant classification graded in a 5-class system, 22 29 nonsense or indel variants expected to lead to a premature termination codon were classified as VUS class 5 (definitely pathogenic), all of them novel except p.R2119*, p.Y3430*, and p.R3792*. [23][24][25] One variant was a new splicing mutation in intron 5 (c.457 1 3A>C) that dramatically decreased the score of the donor splice Patients investigated for mitochondrial network. (Table 2), arguing against a founder effect related to an ancestral mutation.…”

“…Fibroblasts were obtained from arm skin biopsies in 11 patients and in 8 healthy controls including 5 females (18,25,26,27, and 46 years old) and 3 males (21, 43, and 54 years old). Primary culture cells (patient and control fibroblasts) were cultured at 378C in 5% CO 2 in glucose medium consisting of Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum and 100U/ml penicillin/streptomycin.…”

ANO10 c.1150_1151del is a founder mutation causing autosomal recessive cerebellar ataxia in Roma/Gypsies

“…In contrast to AD forms, unravelling the molecular background and genotype-phenotype correlations of AR ataxias has proven to be more complicated, T. Chamova, L. Florez, L. Kalaydjieva and I. Tournev have equal contributions to the work. and the currently known 14 genes do not provide complete coverage for molecular diagnosis and prevention [4].…”

SNP Analysis and Whole Exome Sequencing: Their Application in the Analysis of a Consanguineous Pedigree Segregating Ataxia

“…Homozygosity mapping is a valuable tool for the identification of defective loci, especially in patients born from consanguineous relationships [36], and has been successfully used in cases of ARCA, including ARSACS [37]. However, a high percentage of consanguineous ataxia families have been found to segregate with loci not corresponding to known ataxia genes [37,24], suggesting that further unidentified ARCA entities exist and paving the way for the discovery of novel causative genes [37].…”

“…However, a high percentage of consanguineous ataxia families have been found to segregate with loci not corresponding to known ataxia genes [37,24], suggesting that further unidentified ARCA entities exist and paving the way for the discovery of novel causative genes [37]. …”