Whole genome sequencing in patients with retinitis pigmentosa reveals pathogenic DNA structural changes and NEK2 as a new disease gene

Abstract

We performed whole genome sequencing in 16 unrelated patients with autosomal recessive retinitis pigmentosa (ARRP), a disease characterized by progressive retinal degeneration and caused by mutations in over 50 genes, in search of pathogenic DNA variants. Eight patients were from North America, whereas eight were Japanese, a population for which ARRP seems to have different genetic drivers. Using a specific workflow, we assessed both the coding and noncoding regions of the human genome, including the evaluation of highly polymorphic SNPs, structural and copy number variations, as well as 69 control genomes sequenced by the same procedures. We detected homozygous or compound heterozygous mutations in 7 genes associated with ARRP (USH2A, RDH12, CNGB1, EYS, PDE6B, DFNB31, and CERKL) in eight patients, three Japanese and five Americans. Fourteen of the 16 mutant alleles identified were previously unknown. Among these, there was a 2.3-kb deletion in USH2A and an inverted duplication of ∼446 kb in EYS, which would have likely escaped conventional screening techniques or exome sequencing. Moreover, in another Japanese patient, we identified a homozygous frameshift (p.L206fs), absent in more than 2,500 chromosomes from ethnically matched controls, in the ciliary gene NEK2, encoding a serine/threonineprotein kinase. Inactivation of this gene in zebrafish induced retinal photoreceptor defects that were rescued by human NEK2 mRNA. In addition to identifying a previously undescribed ARRP gene, our study highlights the importance of rare structural DNA variations in Mendelian diseases and advocates the need for screening approaches that transcend the analysis of the coding sequences of the human genome. medical genetics | ophthalmology | ciliopathy | retinal blindness

Identity-by-descent–guided mutation analysis and exome sequencing in consanguineous families reveals unusual clinical and molecular findings in retinal dystrophy

“…Whole-genome sequencing will offer a more suitable detection technique for these mutation mechanisms. 38 In conclusion, our study emphasized that IBD-guided mutation analysis and/or WES is a powerful tool for the molecular diagnosis of RD-even in a single individual. We unmasked unusual molecular and consequent clinical findings-the latter guiding future medical management and prognosis.…”

Whole-genome sequencing overcomes pseudogene homology to diagnose autosomal dominant polycystic kidney disease

“…Our small cohort size is a potential limitation, though the sample size is comparable to other recent disease-cohort based WGS studies and is reflective of the prospective study design. 15,16 Our study is however the first WGS study in any nephrology cohort.…”

“…This affords broad power to detect single-nucleotide variants (SNVs) and small insertions and deletions (indels), and the ability to detect larger copy number variants (CNVs) and structural variants (SVs), such as inversions and translocations. 15,16 Since the introduction of the Illumina HiSeq X sequencing system, the cost of WGS has decreased significantly and is likely to continue to reduce in cost over time.…”

Identification of false-negative mutations missed by next-generation sequencing in retinitis pigmentosa patients: a complementary approach to clinical genetic diagnostic testing

“…As expected, given the extreme genetic heterogeneity of RP, numerous disease-related mutations have been discovered by TES or WES. 3,8 However, almost all current reports focus on single-nucleotide polymorphisms or insertions/deletions detected by NGS, thereby discarding information in uncovered or low-depth regions. Several previous studies of RP briefly reported this phenomenon without detailed investigation or deep discussion.…”

“…6,7 WGS analyzes the entire genome and is especially useful for detecting mutations in noncoding regions, structural variations, and copy-number variations. 8 Both TES and WES are commonly used to detect pathogenic mutations in patients with RP; WGS is less widely used than TES or WES, primarily because of its high cost. Although numerous diseasecausing genes and mutations in RP have recently been identified by TES and WES, a considerable proportion of RP cases seem to lack these pathogenic mutations.…”