Spectrum Analysis of Albinism Genes in a Large Cohort of Chinese Index Patients

Albinism is a genetically heterogeneous trait with a prevalence of 1:17,000 worldwide. At least 22 genes have been identified as the causative genes of albinism in humans. These involved 10 genes in nonsyndromic albinism and 12 syndromic albinism genes (Fernández et al., 2021Fernández A. Hayashi M. Garrido G. Montero A. Guardia A. Suzuki T. et al.Genetics of non-syndromic and syndromic oculocutaneous albinism in human and mouse.Pigment Cell Melanoma Res. 2021; 34: 786-799Crossref PubMed Scopus (18) Google Scholar). Because the disease gene mutation is population specific, it is important to investigate the spectrum of disease gene and allele distribution in the Chinese population for the precise intervention of this disease in their early lives. A total of 1,146 unrelated patients were enrolled from the Chinese population who were clinically diagnosed with albinism by specialists in dermatology and ophthalmology from June 2008 to December 2020, including 858 unreported cases (Supplementary Table S1) and 288 cases that were previously reported (Supplementary Materials and Methods). A pipeline for the mutation screen of all known 22 albinism genes is shown in Figure 1. Two representative cases (one Hermansky–Pudlak syndrome [HPS] 6 [patient 1,041] and one HPS-1 [patient 1,052]) for confirmatory diagnosis are shown in Supplementary Figure S1. Details of methods are described in Supplementary Materials and Methods. The confirmed molecular diagnostic rate with two trans-pathogenic/likely pathogenic alleles was 93.63% (1,073 of 1,146). A total of 63 patients (5.50%) carried only one mutational allele, and 10 patients (0.87%) had no detected pathogenic/likely pathogenic variants. The undetected alleles may be located in the noncoding regions that are missed by the techniques used or may be from unknown albinism genes. Of the 1,073 confirmed cases, oculocutaneous albinism (OCA) 1 is the most common subtype (62.07%) in Chinese, followed by OCA-2 (17.43%) and OCA-4 (10.90%) (Figure 2a and Supplementary Table S2). This spectrum is slightly different from that of our previous pilot study (OCA-1: 70.1%, OCA-4: 12.6%, OCA-2: 10.2%) (Wei et al., 2010Wei A. Wang Y. Long Y. Wang Y. Guo X. Zhou Z. et al.A comprehensive analysis reveals mutational spectra and common alleles in Chinese patients with oculocutaneous albinism.J Invest Dermatol. 2010; 130: 716-724Abstract Full Text Full Text PDF PubMed Scopus (59) Google Scholar). The top three mutational genes in the European population are similar (Lasseaux et al., 2018Lasseaux E. Plaisant C. Michaud V. Pennamen P. Trimouille A. Gaston L. et al.Molecular characterization of a series of 990 index patients with albinism.Pigment Cell Melanoma Res. 2018; 31: 466-474Crossref PubMed Scopus (78) Google Scholar) (Figure 2b and Supplementary Table S2). However, in the Japanese population, OCA-4 is the most common subtype, followed by OCA-1 and HPS-1 (Okamura and Suzuki, 2021Okamura K. Suzuki T. Current landscape of oculocutaneous albinism in Japan.Pigment Cell Melanoma Res. 2021; 34: 190-203Crossref PubMed Scopus (12) Google Scholar) (Figure 2c and Supplementary Table S2). Therefore, we further confirmed that the mutational spectrum of albinism genes is population specific. Except for one patient with OCA-3 (patient 908) who had relatively white skin, all other patients had normal skin pigmentation. The skin color on the body parts exposed to sunlight such as arms and face of most patients (9 of 10) was gradually tanned with age, which is significantly different from other OCA types. In addition, the hair color of six patients darkened with age, and the color of irises darkened too (Supplementary Table S3). We therefore concluded that phenotypes of OCA-3 are mild compared with that of other OCA types in the non-African population. OCA-6 accounts for 3.1% of albinism in the European cohort (Lasseaux et al., 2018Lasseaux E. Plaisant C. Michaud V. Pennamen P. Trimouille A. Gaston L. et al.Molecular characterization of a series of 990 index patients with albinism.Pigment Cell Melanoma Res. 2018; 31: 466-474Crossref PubMed Scopus (78) Google Scholar) but only 0.47% (5 of 1,146) in our screen, suggesting a lower prevalence of OCA-6 in Chinese. To date, 32 patients with OCA-6 have been reported worldwide with variable phenotypes. Our five Chinese patients with OCA-6, including two newly reported cases (patients 1,041 and 1,042) exhibited a relatively mild form of albinism. Syndromic albinism forms must be paid more attention to in patients with albinism because we found 4.80% (55 of 1,146) patients with HPS in this cohort. HPS-1 (28 of 55) is the predominant form of HPS in the Chinese population, followed by HPS-3 (9 of 55) and HPS-6 (9 of 55). Patients with HPS-3, HPS-5, or HPS-6 usually presented only ocular albinism. Because different subtypes of HPS responded differently to the administration of 1-deamino-8-D-arginine vasopressin to prevent bleeding before surgeries (Ma et al., 2016Ma J. Zhang Z. Yang L. Kriston-Vizi J. Cutler D.F. Li W. BLOC-2 subunit HPS6 deficiency affects the tubulation and secretion of von Willebrand factor from mouse endothelial cells.J Genet Genomics. 2016; 43: 686-693Crossref PubMed Scopus (21) Google Scholar), and different HPS subtypes may have variable complications in colitis and pulmonary fibrosis (Fernández et al., 2021Fernández A. Hayashi M. Garrido G. Montero A. Guardia A. Suzuki T. et al.Genetics of non-syndromic and syndromic oculocutaneous albinism in human and mouse.Pigment Cell Melanoma Res. 2021; 34: 786-799Crossref PubMed Scopus (18) Google Scholar). Precise genotyping of HPS subtypes is important. In total, 486 different alleles were identified in this cohort, including 285 alleles reported previously and 199 alleles reported in this study. Among these 199 alleles, 182 were classified as albinism-causative alleles, and 17 were variants of uncertain significance (Supplementary Table S4). In addition to locus heterogeneity, the distribution of variants in each albinism gene is also population specific. Among the mutational alleles of TYR, the c.929_930insC allele was the most common allele with a frequency of 19.97% (271 of 1,357), followed by c.896G>A (239 of 1,357), c.832C>T (134 of 1,357), and other alleles as shown in Figure 2d. The p.T373L, c.1037-7T>A, and c.1A>G were the most frequent alleles in European populations (Lasseaux et al., 2018Lasseaux E. Plaisant C. Michaud V. Pennamen P. Trimouille A. Gaston L. et al.Molecular characterization of a series of 990 index patients with albinism.Pigment Cell Melanoma Res. 2018; 31: 466-474Crossref PubMed Scopus (78) Google Scholar). In Japanese population, the c.929_930insC, p.P431L, and p.R77Q were the most prevalent alleles (Okamura and Suzuki, 2021Okamura K. Suzuki T. Current landscape of oculocutaneous albinism in Japan.Pigment Cell Melanoma Res. 2021; 34: 190-203Crossref PubMed Scopus (12) Google Scholar). The most common OCA2 allele in this screen was p.R136X (31 of 396), followed by c.1182+1G>A (22 of 396) and p.A481T (21 of 396). The most frequent allele of SLC45A2 in this cohort was p.D160H (111 of 246). The distribution of mutational variants clustered on some exons, and some variants showed a founder effect in different populations. In Chinese patients with OCA-1, 82.54% (1,120 of 1,357) of the total TYR mutational alleles were clustered on exons 1 and 2 (Figure 2e), which are the hotspots of TYR mutations in the Chinese population (Wei et al., 2010Wei A. Wang Y. Long Y. Wang Y. Guo X. Zhou Z. et al.A comprehensive analysis reveals mutational spectra and common alleles in Chinese patients with oculocutaneous albinism.J Invest Dermatol. 2010; 130: 716-724Abstract Full Text Full Text PDF PubMed Scopus (59) Google Scholar). In the European population, 63.5% of TYR alleles are located in exons 1 and 4 (Lasseaux et al., 2018Lasseaux E. Plaisant C. Michaud V. Pennamen P. Trimouille A. Gaston L. et al.Molecular characterization of a series of 990 index patients with albinism.Pigment Cell Melanoma Res. 2018; 31: 466-474Crossref PubMed Scopus (78) Google Scholar) (Figure 2f). The p.D160H mutation in SLC45A2 is the most common mutational allele in Chinese patients with OCA-4, which is likely due to a founder effect. In Japanese and Korean patients with OCA-4, the allele with a founder effect is p.D157N (Inagaki et al., 2005Inagaki K. Suzuki T. Ito S. Suzuki N. Fukai K. Horiuchi T. et al.OCA4: evidence for a founder effect for the p.D157N mutation of the MATP gene in Japanese and Korean.Pigment Cell Res. 2005; 18: 385-388Crossref PubMed Scopus (16) Google Scholar). A total of 34.55% (19 of 55) of the total HPS1 mutational alleles were located on exons 11 and 19 of the HPS1 gene, suggesting these exons are the hotspots of HPS1 variants in the Chinese population (Liu et al., 2021Liu T. Yuan Y. Bai D. Qi Z. Yang L. Zhang T. et al.Genetic variants and mutational spectrum of Chinese Hermansky-Pudlak syndrome patients.Pigment Cell Melanoma Res. 2021; 34: 111-121Crossref PubMed Scopus (8) Google Scholar). Genetic screening of the albinism genes in different populations reveals that the definition of nonpathogenic variants or pathological mutations by allelic frequency is population specific. Several common alleles with pathogenic or benign evidence are summarized in Supplementary Table S5. Interestingly, we only found one patient with OCA-1, patient 410, who was diagnosed with metastatic melanoma, suggesting that the incidence of albinism with malignant melanoma in Chinese is very low (1 of 1,146). In summary, in this study, we reported 199 additional albinism-causative alleles, which expands the allelic pool of albinism database. The population-specific distribution of disease genes and alleles is important for precision diagnosis, carrier screening, prenatal diagnosis, and genetic counseling of albinism. No datasets were generated or analyzed during this study. This study was approved by the institutional review board of the bioethics committees of Beijing Tongren Hospital (China) and Beijing Children’s Hospital, Capital Medical University (Beijing, China). The study was conducted according to the Declaration of Helsinki Principles. Written informed consents were signed by all subjects participating in this study or by the parents or guardians of the children. The parents of patients 1,041 and 1,052 consented to the publication of the images in Supplementary Figure S1. Aihua Wei: http://orcid.org/0000-0003-3381-4230 Tianjiao Zhang: http://orcid.org/0000-0001-6777-5722 Yefeng Yuan: http://orcid.org/0000-0003-2651-7182 Zhan Qi: http://orcid.org/0000-0002-2239-4333 Dayong Bai: http://orcid.org/0000-0003-1190-2539 Yingzi Zhang: http://orcid.org/0000-0003-3772-9068 Yunlan Zhang: http://orcid.org/0000-0002-2239-4333 Teng Liu: http://orcid.org/0000-0002-4858-9454 Qiaorong Huang: http://orcid.org/0000-0002-1112-2623 Xiumin Yang: http://orcid.org/0000-0002-6121-1982 Wei Li: http://orcid.org/0000-0002-0248-5510 The authors state no conflict of interest. This work was partially supported by grants from the Ministry of Science and Technology of China (#2016YFC1000306) and the National Natural Science Foundation of China (#31830054 and #82173447). Conceptualization: WL; Data Curation: AW, TZ, YY, ZQ, DB, YiZ, YuZ, TL, QH, XY, WL; Formal Analysis: TZ, YY, ZQ, DB, YiZ, YuZ, TL, QH; Funding Acquisition: AW, WL; Investigation: TZ, YY, ZQ, DB, YiZ, YuZ, TL, QH; Methodology: YY, ZQ, DB, YiZ, YuZ, TL, QH, WL; Project Administration: AW, WL; Supervision: AW, XY, WL; Writing - Original Draft Preparation: AW, TZ; Writing - Review and Editing: WL We recruited 1,146 unrelated patients who were from the Chinese population and diagnosed with albinism clinically by dermatological specialists and ophthalmological specialists from June 2008 to December 2020, including 858 unreported cases and 288 patients who were previously reported (Liu et al., 2021aLiu T. Yuan Y. Bai D. Qi Z. Yang L. 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Li W. et al.Application of multiplex ligation-dependent probe amplification in the genetic testing of oculocutaneous albinism.Chin Med J (Engl). 2019; 132: 2011-2012Crossref PubMed Scopus (3) Google Scholar). The average age of this cohort was about 10 years, ranging from 3 days to 78 years, and male-to-female ratio was 1:0.75. The patients were from all provinces of mainland China except from Tibet and were mostly Han population except 20 patients who were of other ethnic groups. Only three patients (0.26%, 3 of 1,146) had a family history of consanguineous marriage. This study was approved by the institutional review board of the bioethics committees of Beijing Tongren Hospital (China) and Beijing Children’s Hospital, Capital Medical University (Beijing, China). The study was conducted according to the Declaration of Helsinki Principles. Written informed consents were signed by all subjects participating in this study or by the parents or guardians of the children. The parents of patients 1,041 and 1,052 consented to the publication of the images in Supplementary Figure S1. Oculocutaneous albinism (OCA) 1A, OCA1B, and OCA2 were clinically diagnosed on the basis of the clinical features (Wei et al., 2019Wei A. Yuan Y. Qi Z. Liu T. Bai D. Zhang Y. et al.Instability of BLOC-2 and BLOC-3 in Chinese patients with Hermansky-Pudlak syndrome.Pigment Cell Melanoma Res. 2019; 32: 373-380Crossref PubMed Scopus (14) Google Scholar, Wei et al., 2016Wei A. Yuan Y. Bai D. Ma J. Hao Z. Zhang Y. et al.NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients.Pigment Cell Melanoma Res. 2016; 29: 702-706Crossref PubMed Scopus (29) Google Scholar). These included the dermatological phenotypes (skin color and hair color at birth and at the time of counseling), the ophthalmological phenotypes (eye color, translucent irises, presence of visual impairment, photophobia, nystagmus, and foveal hypoplasia), and symptoms in support of a syndromic form of albinism (bleeding tendency, granulomatous colitis, pulmonary fibrosis, predisposition to infections). Patients recruited in this study all had the symptoms of nystagmus and at least one other ocular feature of albinism (translucent irises, foveal hypoplasia). Patients with Hermansky–Pudlak syndrome (HPS) were confirmed by the absence of platelet-dense granules by whole-mount electron microscopy and destabilized HPS proteins by western blotting (Wei et al., 2019Wei A. Yuan Y. Qi Z. Liu T. Bai D. Zhang Y. et al.Instability of BLOC-2 and BLOC-3 in Chinese patients with Hermansky-Pudlak syndrome.Pigment Cell Melanoma Res. 2019; 32: 373-380Crossref PubMed Scopus (14) Google Scholar, Wei et al., 2016Wei A. Yuan Y. Bai D. Ma J. Hao Z. Zhang Y. et al.NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients.Pigment Cell Melanoma Res. 2016; 29: 702-706Crossref PubMed Scopus (29) Google Scholar). Parents of the patients participated in this study when they consented. Clinical features, pathogenicity of variants, recessive trans-transmitted alleles or dominant de novo mutations in segregation analysis, and functional assays are the four key components to confirm the molecular diagnosis of albinism subtypes. Before 2016, 509 patients were analyzed by direct Sanger sequencing to detect the entire coding exons and the exon/intronic flanking regions of one or several common albinism genes (TYR, OCA2, TYRP1, SLC45A2, HPS1, or GPR143) (Wei et al., 2011Wei A. Yang X. Lian S. Li W. Implementation of an optimized strategy for genetic testing of the Chinese patients with oculocutaneous albinism.J Dermatol Sci. 2011; 62: 124-127Abstract Full Text Full Text PDF PubMed Scopus (33) Google Scholar, Wei et al., 2010Wei A. Wang Y. Long Y. Wang Y. Guo X. Zhou Z. et al.A comprehensive analysis reveals mutational spectra and common alleles in Chinese patients with oculocutaneous albinism.J Invest Dermatol. 2010; 130: 716-724Abstract Full Text Full Text PDF PubMed Scopus (71) Google Scholar). Total genomic DNA was extracted from blood samples using the routine proteinase K/SDS method. Standard PCR amplification procedures were used with an annealing temperature of 58‒59 °C for all primers. Primer sequences are available on request. Since 2016, next-generation sequencing was implemented in genetic testing of 637 patients (Liu et al., 2021aLiu T. Yuan Y. Bai D. Qi Z. Yang L. Zhang T. et al.Genetic variants and mutational spectrum of Chinese Hermansky-Pudlak syndrome patients.Pigment Cell Melanoma Res. 2021; 34: 111-121Crossref PubMed Scopus (11) Google Scholar; Wei et al., 2016Wei A. Yuan Y. Bai D. Ma J. Hao Z. Zhang Y. et al.NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients.Pigment Cell Melanoma Res. 2016; 29: 702-706Crossref PubMed Scopus (29) Google Scholar). In trio whole-exome sequencing, exon-containing fragments were enriched with the Agilent Sure Select Human All Exon V6 kit (Santa Clara, CA), and the mutation was detected using the Illumina high-throughput sequencing platform. Sanger sequencing was used to verify all the candidate pathogenic variants and the origin from their parents. For the copy number variants implicated by next-generation sequencing, multiplex ligation‒dependent probe amplification or qPCR was further used to detect the possible large fragment heterozygosity deletion (Wei et al., 2016Wei A. Yuan Y. Bai D. Ma J. Hao Z. Zhang Y. et al.NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients.Pigment Cell Melanoma Res. 2016; 29: 702-706Crossref PubMed Scopus (29) Google Scholar; Zhang et al., 2019bZhang Y.Z. Bai D.Y. Qi Z. Zhao S.Z. Yang X.M. Li W. et al.Application of multiplex ligation-dependent probe amplification in the genetic testing of oculocutaneous albinism.Chin Med J (Engl). 2019; 132: 2011-2012Crossref PubMed Scopus (3) Google Scholar). Multiplex ligation‒dependent probe amplification was performed for 20 patients with identified homozygous variants in TYR or OCA2 with unknown parental origin or single heterozygous pathogenic variants in TYR or OCA2. qPCR was used to detect large deletions of heterozygosity in three patients identified to possess one pathogenic variant in HPS1 or SLC45A2. Electron microscopy was used to observe platelet-dense granules. Detailed procedures of electron microscopy examination on whole-mount platelets have been described previously (Wei et al., 2019Wei A. Yuan Y. Qi Z. Liu T. Bai D. Zhang Y. et al.Instability of BLOC-2 and BLOC-3 in Chinese patients with Hermansky-Pudlak syndrome.Pigment Cell Melanoma Res. 2019; 32: 373-380Crossref PubMed Scopus (14) Google Scholar, Wei et al., 2016Wei A. Yuan Y. Bai D. Ma J. Hao Z. Zhang Y. et al.NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients.Pigment Cell Melanoma Res. 2016; 29: 702-706Crossref PubMed Scopus (29) Google Scholar). Platelets from 2-ml peripheral blood were isolated and lysed. Western blotting was used to detect the steady-state levels of HPS proteins, with detailed procedures described previously (Wei et al., 2019Wei A. Yuan Y. Qi Z. Liu T. Bai D. Zhang Y. et al.Instability of BLOC-2 and BLOC-3 in Chinese patients with Hermansky-Pudlak syndrome.Pigment Cell Melanoma Res. 2019; 32: 373-380Crossref PubMed Scopus (14) Google Scholar, Wei et al., 2016Wei A. Yuan Y. Bai D. Ma J. Hao Z. Zhang Y. et al.NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients.Pigment Cell Melanoma Res. 2016; 29: 702-706Crossref PubMed Scopus (29) Google Scholar). The GRCh37/UCSChg19 was used as a reference genome to compare and annotate the variants. For a previously unreported variant or variant included in the Human Gene Mutation Database, the pathogenicity was evaluated by following the guidelines of the American College of Medical Genetics and Genomics (Richards et al., 2015Richards S. Aziz N. Bale S. Bick D. Das S. Gastier-Foster J. et al.Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.Genet Med. 2015; 17: 405-424Abstract Full Text Full Text PDF PubMed Scopus (17784) Google Scholar). Download .pdf (1.76 MB) Help with pdf files Supplementary Tables 1–5