A phased SNP-based classification of sickle cell anemia HBB haplotypes

Elmutaz M Shaikho,Martin H Steinberg,Gustavo Mostoslavsky,Amein K Al-Ali,Maria Stella Figueiredo,David H.K Chui,Paola Sebastiani,George J Murphy,Abdulrahman Alsultan,Hatem Qutub,John J Farrell,Lindsay A Farrer

doi:10.1186/s12864-017-4013-y

Abstract

BackgroundSickle cell anemia causes severe complications and premature death. Five common β-globin gene cluster haplotypes are each associated with characteristic fetal hemoglobin (HbF) levels. As HbF is the major modulator of disease severity, classifying patients according to haplotype is useful. The first method of haplotype classification used restriction fragment length polymorphisms (RFLPs) to detect single nucleotide polymorphisms (SNPs) in the β-globin gene cluster. This is labor intensive, and error prone.MethodsWe used genome-wide SNP data imputed to the 1000 Genomes reference panel to obtain phased data distinguishing parental alleles.ResultsWe successfully haplotyped 813 sickle cell anemia patients previously classified by RFLPs with a concordance >98%. Four SNPs (rs3834466, rs28440105, rs10128556, and rs968857) marking four different restriction enzyme sites unequivocally defined most haplotypes. We were able to assign a haplotype to 86% of samples that were either partially or misclassified using RFLPs.ConclusionPhased data using only four SNPs allowed unequivocal assignment of a haplotype that was not always possible using a larger number of RFLPs. Given the availability of genome-wide SNP data, our method is rapid and does not require high computational resources.

Highlights

Sickle cell anemia causes severe complications and premature death
Haplotype classification Of 371 CSSCD patients classified as BEN/BEN using five restriction fragment length polymorphisms (RFLPs), we achieved a concordance of 98% (367/371) using four phased single nucleotide polymorphisms (SNPs)
For BEN/SEN, BEN/CAM, CAR/CAR, CAR/SEN, CAR/ CAM, CAR/Arab Indian (AI), SEN/SEN, SEN/CAM, SEN/AI, and CAM/CAM haplotypes our concordance with the RFLP method was 100% the numbers of patients in each category was smaller

Summary

Introduction

Sickle cell anemia causes severe complications and premature death. Five common β-globin gene cluster haplotypes are each associated with characteristic fetal hemoglobin (HbF) levels. The first method of haplotype classification used restriction fragment length polymorphisms (RFLPs) to detect single nucleotide polymorphisms (SNPs) in the β-globin gene cluster. This is labor intensive, and error prone. Haplotypes of sickle cell anemia were first ascertained by analysis of restriction fragment length polymorphisms (RFLPs) in the HBB gene cluster [7]. This classification was based on detecting whether or not cleavage occurred at five to eight restriction sites when DNA was digested with restriction endonucleases, as shown in Fig. 1 [8,9,10]. The phased GWAS data allowed assigning SNPs to parental chromosomes, which facilitated the classification procedure using fewer SNPs

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Discussion

Conclusion