Screening for potential undiagnosed Gaucher disease patients: Utilisation of the Gaucher earlier diagnosis consensus point-scoring system (GED-C PSS) in conjunction with electronic health record data, tissue specimens, and small nucleotide polymorphism (SNP) genotype data available in Finnish biobanks

Abstract

Background: Autosomal recessive Gaucher disease (GD) is likely underdiagnosed in many countries. Because the number of diagnosed GD patients in Finland is relatively low, and the true prevalence is currently not known, it was hypothesized that undiagnosed GD patients may exist in Finland. Our previous study demonstrated the applicability of Gaucher Earlier Diagnosis Consensus point-scoring system (GED-C PSS; Mehta et al., 2019) and Finnish biobank data and specimens in the automated point scoring of large populations. An indicative point-score range for Finnish GD patients was determined, but undiagnosed patients were not identified partly due to high number of high-score subjects in combination with a lack of suitable samples for diagnostics in the assessed biobank population. The current study extended the screening to another biobank and evaluated the feasibility of utilising the automated GED-C PSS in conjunction with small nucleotide polymorphism (SNP) chip genotype data from the FinnGen study of biobank sample donors in the identification of undiagnosed GD patients in Finland. Furthermore, the applicability of FFPE tissues and DNA restoration in the next-generation sequencing (NGS) of the GBA gene were tested.

Methods: Previously diagnosed Finnish GD patients eligible to the study, and up to 45,100 sample donors in Helsinki Biobank (HBB) were point scored. The GED-C point scoring, adjusted to local data, was automated, but also partly manually verified for GD patients. The SNP chip genotype data for rare GBA variants was visually assessed. FFPE tissues of GD patients were obtained from HBB and Biobank Borealis of Northern Finland (BB).

Results: Three previously diagnosed GD patients and one patient previously treated for GD-related features were included. A genetic diagnosis was confirmed for the patient treated for GD-related features. The GED-C point score of the GD patients was 12.5-22.5 in the current study. The score in eight Finnish GD patients of the previous and the current study is thus 6-22.5 points per patient. In the automated point scoring of the HBB subpopulation (N ≈ 45,100), the overall scores ranged from 0 to 17.5, with 0.77% (346/45,100) of the subjects having ≥10 points. The analysis of SNP chip genotype data was able to identify the diagnosed GD patients, but potential undiagnosed patients with the GED-C score and/or the GBA genotype indicative of GD were not discovered. Restoration of the FFPE tissue DNA improved the quality of the GBA NGS, and pathogenic GBA variants were confirmed in five out of six unrestored and in all four restored FFPE DNA samples.

Discussion: These findings imply that the prevalence of diagnosed patients (~1:325,000) may indeed correspond the true prevalence of GD in Finland. The SNP chip genotype data is a valuable tool that complements the screening with the GED-C PSS, especially if the genotyping pipeline is tuned for rare variants. These proof-of-concept biobank tools can be adapted to other rare genetic diseases.

Keywords: BB, Biobank Borealis of Northern Finland; Biobank study; DF4/DF5, Data freeze 4/5; EHR, Electronic health record; Electronic health record data; FFPE, Formalin-fixed, paraffin embedded; GBA; GBA1/GBA, β-glucocerebrosidase gene; GD, Gaucher disease; GED-C, Gaucher Earlier Diagnosis Consensus; Gaucher disease; Gaucher earlier diagnosis consensus point-scoring system; GlcCer, β-glucosylceramide; GlcCerase, β-glucosylceramidase; GlcSph/Lyso-Gb1, β-glucosylsphingosine; HBB, Helsinki Biobank; HUH, Helsinki University Hospital; HUS, Hospital District of Helsinki and Uusimaa; ICD-10, International Statistical Classification of Diseases and Related Health Problems 10th Revision; NGS, Next-generation sequencing; OUH, Oulu University Hospital; PSS, Point-scoring system; SNP, small nucleotide polymorphism; Small nucleotide polymorphism chip genotype data; VUS, variant of uncertain significance.

Fig. 1

A summary of the formation of the final cohorts 1–4. Subjects of the cohort 1 and 2 represented patients previously diagnosed with or examined for features of Gaucher disease (GD) in Helsinki University Hospital (HUH) and who had samples/sample-derived data available in Helsinki Biobank (HBB). In addition, patients with known GBA variant status [15] and diagnosed with GD in Oulu University Hospital (OUH) with formalin-fixed, paraffin-embedded (FFPE) tissue samples available in Biobank Borealis (BB) were included to increase the number of samples in the cohort 3. Samples of the subjects of the cohort 1 have been analysed in the FinnGen study and are thus included in the final cohort 4 with genotype data as well as electronic health record (EHR) data available in Hospital District of Helsinki and Uusimaa (HUS) (indicated by an asterisk).

Fig. 2

A workflow of the screening for potential undiagnosed Gaucher disease (GD) patients in Helsinki Biobank (HBB). Both the automated GED-C point scoring and small nucleotide polymorphism (SNP) chip genotype data from the FinnGen study were utilised. Two genotype data sets were employed due to release schedules of the raw data (Data freeze 4 and 5).

Fig. 3

Cluster plots generated from small nucleotide polymorphism (SNP) genotype data of Helsinki Biobank samples genotyped in the FinnGen study [18]. The plots shown here include the samples of the three previously diagnosed Gaucher disease patients identified in Helsinki Biobank and eligible to the study (HBB1–HBB3 in A–C, respectively; marked with pink circles). One plot corresponds to one variant, while one spot in each plot corresponds to one sample. The colour of the spots and ellipses indicate the computed genotype result and cluster boundaries, respectively, as determined by the SNP chip calling algorithm. The algorithm is not reliable for genotyping rare variants.

Fig. 4

The GED-C point-score distribution in Helsinki Biobank (HBB) subpopulations representing all HBB sample donors who have been genotyped in the FinnGen study and who have electronic health record data in the records of the Hospital District of Helsinki and Uusimaa (N ≈ 45,100; black columns), and in respective subgroups of individuals suspected (N = 55; yellow columns) or negative (N = 4,670; grey columns) for the GBA hot spot variants c.1448 T > C or c.1226A > G accompanied by the separately indicated point scores of the previously diagnosed GD patients who were identified in HBB and eligible to the study, and who have also been genotyped in the FinnGen (N = 3; red data points). The point scoring of all samples was carried out in an automated manner. The main image shows the distribution of values (rounded to closest integer) among all assessed subjects while the insert represents subjects with a score of ≥10 (n = 346).