Here, we gave a clinical and genetic description of two sisters affected by two different disorders: ALS disease and CHARGE syndrome. In our family, one sister, a 43-year-old woman, was clinically ALS diagnosed, with bulbar onset, pyramidal impairment and spastic phenotype. The second one, a full-termed 41-year-old female, carrying the
CHD7 de novo W2672* mutation, presented typical CHARGE syndrome defects. Although a 2–3% recurrence risk is suggested for children of clinically unaffected parents, attributed to parental germline mosaicism [
28], we excluded any possible mosaicism in both parents, as revealed by sequence analysis. The mutation, located in the BRK domain of unknown function, was already reported by Jongmans et al. [
29], but without any related clinical description and segregation analysis. Anyway, according to data reported in literature by which
CHD7 mutations occur de novo in the vast majority of the typical patients, we assess that the patient carrying this mutation completely fulfill the clinical CHARGE diagnostic criteria [
30,
31]. In CHARGE syndrome, basic research has demonstrated that CHD protein complexes affect chromatin structure and gene expression, thus playing an important role in regulating embryonic development; moreover, being assumed CHD7 protein most likely controls gene expression by chromatin remodelling, functioning as a transcription regulator that binds preferentially to methylated histones in enhancer regions and near transcription sites [
32], it is clear that CHD7 expression is lowered in the presence of an incomplete and/or not functional protein. Haploinsufficiency for CHD7 is the most likely pathogenic mechanism of this syndrome [
33,
34]. Furthermore, epigenetic modifications, including DNA methylation, appear to be involved in motor process influenced by the interaction between genes and environment, and a fraction of those changes might even be transmitted to the offspring [
35]. To date, CHARGE and ALS pathologies never occurred together in the same family and no putative correlation between them has been reported on PubMed Central, but whereas many clinical CHARGE features are shared by other syndrome [
36‐
38] we initially hypothesized a possible link between these two diseases. The detection of the
CHD7 de novo mutation in one sister fully explaining her phenotype, disagreed with our starting hypothesis. This evidence prompted us to focus on variants in ALS patient, comparing NGS results between the two sisters. Nonetheless 152 out of the 380 variants were shared by both sisters, this is slightly less than one would expect: we all share 50% of our variants with each of our siblings. That the CHARGE sister has less, might be explained by the fact that she does not have ALS. So the most interesting variants were those that are unique for the ALS patient. Due to roughly 50% of ALS families remain unexplained after routine genetic testing, in addition to ALS caused by mutations in above-mentioned genes, NGS analysis could contribute in identifying rare variants and/or non-coding-variants causing or increasing the risk of the disease. In addition, the very high fold coverage of sequenced fragments obtained by this technology allows for excluding low-grade mosaicism [
39]. Anyway, being assumed that genetic aetiology of ALS is responsible for one-third of familial disease, it is unknown how much of the remaining of sporadic cases is genetic and how much is due to other factors such as environmental exposures, aging or lifestyle choices. In CHARGE syndrome, too, epigenetic events have recently emerged as important contributors to the disorder [
40]. Anyway, in our case, both in ALS and CHARGE patient NGS analysis revealed no suggestive uncommon variations and no deleterious variants were detected (Supplementary Table B). Indeed, bioinformatical tools (PolyPhen-2, SIFT, LRT, MutationTaster, MutationAssessor, FATHMM, CADD, GERP++) used for analyzing coding missense variants identified in the ALS patient in known ALS genes, predicted no significant scores for damaging effects (data not showed). Among these, we focused on the rs 80,019,660 related to Paraoxonase 1 gene (PON1; c.C602T in exon 6; ref. sEq. NM_000446), the only exonic variant with a MAF of 0.0008. PON 1 has a major protective role both against environmental toxins and as part of the antioxidant defense system and genetic variation across the paroxanase loci may be susceptibility factors for sALS (
http://alsod.iop.kcl.ac.uk). Segregation analysis revealed the presence of this polymorphism only in the father of affected sisters. Moreover, the complexity of the genetic architecture of ALS, including an important role for rare genetic variants, has transformed the way we think about this disease. A significant part of ALS heritability cannot be easily explained by only considering a monogenic model, while interactions between multiple ALS genes might explain the considerable phenotypic variability observed among ALS individuals and this leads us to reconsider the traditional classification system for this disease towards a molecular taxonomy for ALS patients’ stratification [
41]. To verify whether any genetic variants have any role in the pathogenesis of our ALS patient, further deep investigation by whole genome analysis might be useful.