CD59 gene: 143 haplotypes of 22,718 nucleotides length by computational phasing in 113 individuals from different ethnicities

Abstract

Background: CD59 deficiency due to rare germline variants in the CD59 gene causes disabilities, ischemic strokes, neuropathy, and hemolysis. CD59 deficiency due to common somatic variants in the PIG-A gene in hematopoietic stem cells causes paroxysmal nocturnal hemoglobinuria. The ISBT database lists one nonsense and three missense germline variants that are associated with the CD59-null phenotype. To analyze the genetic diversity of the CD59 gene, we determined long-range CD59 haplotypes among individuals from different ethnicities.

Methods: We determined a 22.7 kb genomic fragment of the CD59 gene in 113 individuals using next-generation sequencing (NGS), which covered the whole NM_203330.2 mRNA transcript of 7796 base pairs. Samples came from an FDA reference repository and our Ethiopia study cohorts. The raw genotype data were computationally phased into individual haplotype sequences.

Results: Nucleotide sequencing of the CD59 gene of 226 chromosomes identified 216 positions with single nucleotide variants. Only three haplotypes were observed in homozygous form, which allowed us to assign them unambiguously as experimentally verified CD59 haplotypes. They were also the most frequent haplotypes among both cohorts. An additional 140 haplotypes were imputed computationally.

Discussion: We provided a large set of haplotypes and proposed three verified long-range CD59 reference sequences, based on a population approach, using a generalizable rationale for our choice. Correct long-range haplotypes are useful as template sequences for allele calling in high-throughput NGS and precision medicine approaches, thus enhancing the reliability of clinical diagnostics. Long-range haplotypes can also be used to evaluate the influence of genetic variation on the risk of transfusion reactions or diseases.

Trial registration: ClinicalTrials.gov NCT01282021.

Keywords: blood group genomics; hematology – red cells; immunohematology.

FIGURE 1

CD59 haplotypes observed in the study. The six most common haplotypes (CD59H01 to CD59H06) were observed 5 to 14 times among the 226 chromosomes of the 113 individuals (A). The relative observations among three ethnicities differed (B). The remaining 137 haplotypes for a total of 143 unique haplotypes were observed three times each or less (see Figure 2 and Supplementary material file S3). FDA (orange) and Ethiopia cohorts (yellow); and Caucasian (blue), African American (green) and Ethiopian (African) ethnicities (red). [Color figure can be viewed at wileyonlinelibrary.com]

FIGURE 2

Distribution of CD59 haplotypes in two cohorts. The FDA cohort had a total of 70 haplotype (A) and 80 were found in the Ethiopian cohort (B). Number of CD59 haplotype observations: ≥5 (blue), 4 (yellow), 3 (green), 2 (red), and 1 (gray). [Color figure can be viewed at wileyonlinelibrary.com]