Next-generation sequencing-based molecular diagnosis of a Chinese patient cohort with autosomal recessive retinitis pigmentosa

Abstract

Purpose: Retinitis pigmentosa (RP) is a highly heterogeneous genetic disease; therefore, an accurate molecular diagnosis is essential for appropriate disease treatment and family planning. The prevalence of RP in China had been reported at 1 in 3800, resulting in an estimated total of 340,000 Chinese RP patients. However, genetic studies of Chinese RP patients have been very limited. To date, no comprehensive molecular diagnosis has been done for Chinese RP patients. With the emergence of next-generation sequencing (NGS), comprehensive molecular diagnosis of RP is now within reach. The purpose of this study was to perform the first NGS-based comprehensive molecular diagnosis for Chinese RP patients.

Methods: Thirty-one well-characterized autosomal recessive RP (arRP) families were recruited. For each family, the DNA sample from one affected member was sequenced using our custom capture panel, which includes 163 retinal disease genes. Variants were called, filtered, and annotated by our in-house automatic pipeline.

Results: Twelve arRP families were successfully molecular diagnosed, achieving a diagnostic rate of approximately 40%. Interestingly, approximately 63% of the pathogenic mutations we identified are novel, which is higher than that observed in a similar study on European descent (45%). Moreover, the clinical diagnoses of two families were refined based on the pathogenic mutations identified in the patients.

Conclusions: We conclude that comprehensive molecular diagnosis can be vital for an accurate clinical diagnosis of RP. Applying this tool on patients from different ethnic groups is essential for enhancing our knowledge of the global spectrum of RP disease-causing mutations.

Keywords: Chinese population; molecular diagnosis; next-generation sequencing; retinitis pigmentosa.

Figure 1

Schematic chart shows the stepwise strategy to identify pathogenic mutation.

Figure 2

Three families (4279, 4283, and 4285) carry known pathogenic mutations in known RP genes. (A–C) The segregation results of the three families. The genotype of each evaluated individual is shown below the individual's symbol. Wild type is listed as a “+.” (D) Multispecies alignment shows the conservation of the amino acid affected by the novel missense mutation. Red box shows the affected amino acid.

Figure 3

Four families (4264, 4277, 4282, and 4295) carry novel severe loss-of-function mutations in known RP genes. (A–D) The segregation results of the four families. The genotype of each evaluated individual is shown below the individual's symbol. Wild type is listed as a “+.”

Figure 4

Two families (4268 and 4294) carry presumably damaging missense mutations in known RP genes. (A, C) The segregation results of the two families. The genotype of each evaluated individual is shown below the individual's symbol. Wild type is listed as a “+.” (B, D) Multispecies alignments show the conservation of the amino acids affected by the novel missense mutations. Red boxes show the affected amino acids.

Figure 5

Three families (4274, 4293, and 4263) carry putative pathogenic mutations in other retinal disease genes. (A–C) The segregation results of the three families. (D) Multispecies alignment shows the conservation of the amino acid affected by the novel missense mutation. Red box shows the affected amino acid.