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dc.contributor.authorShaikho, Elmutaz M.
dc.contributor.authorFarrell, John J.
dc.contributor.authorAlsultan, Abdulrahman
dc.contributor.authorQutub, Hatem
dc.contributor.authorAl-Ali, Amein K.
dc.contributor.authorFigueiredo, Maria Stella [UNIFESP]
dc.contributor.authorChui, David H. K.
dc.contributor.authorFarrer, Lindsay A.
dc.contributor.authorMurphy, George J.
dc.contributor.authorMostoslavsky, Gustavo
dc.contributor.authorSebastiani, Paola
dc.contributor.authorSteinberg, Martin H.
dc.identifier.citationBmc Genomics. London, v. 18, p. -, 2017.
dc.description.abstractBackground: Sickle cell anemia causes severe complications and premature death. Five common beta-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 beta-globin gene cluster. This is labor intensive, and error prone. Methods: We used genome-wide SNP data imputed to the 1000 Genomes reference panel to obtain phased data distinguishing parental alleles. Results: We 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. Conclusion: Phased 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.en
dc.description.sponsorshipNIH Bethesda, MD
dc.publisherBiomed Central Ltd
dc.rightsAcesso aberto
dc.subjectSickle cellen
dc.subjectHaplotype classificationen
dc.titleA phased SNP-based classification of sickle cell anemia HBB haplotypesen
dc.description.affiliationBoston Univ, Sch Med, Dept Med, 72 E Concord St, Boston, MA 02118 USA
dc.description.affiliationBoston Univ, Bioinformat Program, Boston, MA 02215 USA
dc.description.affiliationKing Saud Univ, Coll Med, Sickle Cell Dis Res Ctr, Riyadh, Saudi Arabia
dc.description.affiliationKing Saud Univ, Coll Med, Dept Pediat, Riyadh, Saudi Arabia
dc.description.affiliationKing Faisal Univ, Al Omran Sci Chair, Al Hasa, Saudi Arabia
dc.description.affiliationImam Abdulrahman bin Faisal Univ, Inst Res & Med Consultat, Dammam, Saudi Arabia
dc.description.affiliationEscola Paulista Med, Hematol & Blood Transfus Div, São Paulo, Brazil
dc.description.affiliationBoston Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02118 USA
dc.description.affiliationUnifespEscola Paulista Med, Hematol & Blood Transfus Div, São Paulo, Brazil
dc.description.sponsorshipIDNIH: R01 HL 068970
dc.description.sponsorshipIDNIH: RC2 HL 101212
dc.description.sponsorshipIDNIH: R01 87681
dc.description.sponsorshipIDNIH: T32 HL007501
dc.description.sourceWeb of Science
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