Whole-Genome Sequencing in Diagnostics of Selected Slovenian Undiagnosed Patients with Rare Disorders

Abstract

Several patients with rare genetic disorders remain undiagnosed following comprehensive diagnostic testing using whole-exome sequencing (WES). In these patients, pathogenic genetic variants may reside in intronic or regulatory regions or they may emerge through mutational mechanisms not detected by WES. For this reason, we implemented whole-genome sequencing (WGS) in routine clinical diagnostics of patients with undiagnosed genetic disorders and report on the outcome in 30 patients. Criteria for consideration included (1) negative WES, (2) a high likelihood of a genetic cause for the disorders, (3) positive family history, (4) detection of large blocks of homozygosity or (5) detection of a single pathogenic variant in a gene associated with recessive conditions. We successfully discovered a causative genetic variant in 6 cases, a retrotranspositional event in the APC gene, non-coding variants in the intronic region of the OTC gene and the promotor region of the UFM1 gene, repeat expansion in the RFC1 gene and a single exon duplication in the CNGB3 gene. We also discovered one coding variant, an indel, which was missed by variant caller during WES data analysis. Our study demonstrates the impact of WGS in the group of patients with undiagnosed genetic diseases after WES in the clinical setting and the diversity of mutational mechanisms discovered, which would remain undetected using other methods.

CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements

“…Despite the wide use of exome and genome sequencing, a large number of individuals with inherited disorders lack a genetic diagnosis [36,37]. While there are still novel factors to be discovered, various studies highlight the importance of noncoding regions in human disease [17,[38][39][40]. One important class of functional sequences located in noncoding regions are regulatory elements that can be predicted based on evolutionary conservation, open chromatin state, the three-dimensional structure of chromatin, and other approaches [20,27,41].…”

Four New Cases of Hypomyelinating Leukodystrophy Associated with the UFM1 c.-155_-153delTCA Founder Mutation in Pediatric Patients of Roma Descent in Hungary

“…By adding the phenotypic and molecular data of a further four patients to the 19 described to date [ 7 , 8 , 9 , 10 ], we aimed to expand the clinical and molecular knowledge on this rare entity. We did not see a geographical accumulation of the patients within Hungary; they originated from different parts of the country.…”

“…This homozygous 3-bp deletion in the promoter of the UFM1 gene has further been described in other patients with AR Hypomyelinating leukodystrophy type 14, presenting with microcephaly, hearing impairment, seizures, and global developmental delay, co-segregating in affected sibling and detected by genome sequencing (reported as NM_001286704.1( UFM1 ):c.-273_-271del) [ 8 ] in Pakistani (reported as NC_000013.10 (NM_016617.2):c.-155_-153del) [ 9 ] and Slovenian patient(s) with progressive neurodegenerative disease (reported as NM_016617.2( UFM1 ):c.-155delTCA) [ 10 ]. The Slovenian patient had profound intellectual disability and epilepsy with a history of apnoeic episodes and feeding difficulties in infancy.…”

A guide for the diagnosis of rare and undiagnosed disease: beyond the exome

“…Some of these challenges can be addressed by genome sequencing (GS) [31,33,35,36]. GS can identify canonical [37,38] and complex structural variants [39,40], tandem repeats [37,38], intronic variants [37,38], and coding variants that may not be accurately captured by ES. GS has enabled identification of the causative variants for many undiagnosed cases where prior ES was either unrevealing [38,41] or had provided only partial diagnosis (the causative variant explained only some phenotypes of the patient) [42].…”

“…GS can identify canonical [37,38] and complex structural variants [39,40], tandem repeats [37,38], intronic variants [37,38], and coding variants that may not be accurately captured by ES. GS has enabled identification of the causative variants for many undiagnosed cases where prior ES was either unrevealing [38,41] or had provided only partial diagnosis (the causative variant explained only some phenotypes of the patient) [42]. Diagnosis mediated by GS has also opened avenues for therapy in some cases by identifying the disease mechanism and potential drug targets [42][43][44].…”