Comprehensive molecular diagnosis of 67 Chinese Usher syndrome probands: high rate of ethnicity specific mutations in Chinese USH patients

Abstract

Background: Usher syndrome (USH) is the most common disease causing combined deafness and blindness. It is predominantly an autosomal recessive genetic disorder with occasionally digenic cases. Molecular diagnosis of USH patients is important for disease management. Few studies have tried to find the genetic cause of USH in Chinese patients. This study was designed to determine the mutation spectrum of Chinese USH patients.

Methods: We applied next generation sequencing to characterize the mutation spectrum in 67 independent Chinese families with at least one member diagnosed with USH. Blood was collected at Peking Union Medical College Hospital. This cohort is one of the largest USH cohorts reported. We utilized customized panel and whole exome sequencing, variant analysis, Sanger validation and segregation tests to find disease causing mutations in these families.

Results: We identified biallelic disease causing mutations in known USH genes in 70 % (49) of our patients. As has been previously reported, MYO7A is the most frequently mutated gene in our USH type I patients while USH2A is the most mutated gene in our USH type II patients. In addition, we identify mutations in CLRN1, DFNB31, GPR98 and PCDH15 for the first time in Chinese USH patients. Together, mutations in CLRN1, DNFB31, GPR98 and PCDH15 account for 11.4 % of disease in our cohort. Interestingly, although the spectrum of disease genes is quite similar between our Chinese patient cohort and other patient cohorts from different (and primarily Caucasian) ethnic backgrounds, the mutations themselves are dramatically different. In particular, 76 % (52/68) of alleles found in this study have never been previously reported. Interestingly, we observed a strong enrichment for severe protein truncating mutations expected to have severe functional consequence on the protein in USH II patients compared to the reported mutation spectrum in RP patients, who often carry partial protein truncating mutations.

Conclusions: Our study provides the first comprehensive genetic characterization of a large collection of Chinese USH patients. Up to 90 % of USH patients have disease caused by mutations in known USH disease genes. By combining NGS-based molecular diagnosis and patient clinical information, a more accurate diagnosis, prognosis and personalized treatment of USH patients can be achieved.

Fig. 1

Pedigrees of non-simplex and consanguineous families and sample example figures of clinical data. a Pedigrees of non-simplex and consanguineous families. USH patients are illustrated by squares or circles in black while the unaffected family members are in white. Patients with DNA sequenced by panel or whole exome sequencing in our project are indicated by an arrow. b Fundus of left eye of USHsrf59 at age 31. The fundus showed salt and pepper pigmentation variation in the periphery retina and attenuation of the retinal vessels. c OCT of left eye of USHsrf59 at age 31. OCT showed lack of IS/OS except macula fovea in photoreceptor layer. Her visual acuity is 0.8/0.5 at age 31. This patient was diagnosed with USH II. Her hearing loss began at age 5 and vision loss began at age 12. d Fundus of right eye of USHsrf66 at age 57. The fundus showed bone spicule pigmentation variation and attenuation of the retinal vessels. e OCT of left eye of USHsrf66 at age 57. Her visual acuity is 0.06/0.06 at age 57. OCT showed a thinned retinal pigment epithelium and a photoreceptor layer (lack of IS/OS). This patient was diagnosed with USH II. Her hearing loss began at age 8 and vision loss began at age 30 with night blindness starting from school age. f Hearing test on left ear of USHsrf66

Fig. 2

Another sample figure title Summary of mutations identified in USH genes. a Genes mutated in USH I patients. b Genes mutated in USH II patients

Fig. 3

Double compound heterozygous mutations in patient USHsrf40. Patient USHsrf40 carries compound heterozygous mutations in two genes MYO7A and CGNA1: two missense mutation in MYO7A and frameshift and missense mutations in CNGA1. Mutations segregate in this family

Fig. 4

USH patients are highly enriched in patients with two severe alleles. Patients with USH2A mutations were classified based on number of severe alleles (frameshift mutations, splicing site mutations and nonsense mutations). Enrichment of patients with two severe mutations is significant (Fisher exact test, p-value < 0.0001) in two independent USH patients cohorts (USH patients in this study [30]) compared to that of RP patients