Full‐length nucleotide sequence of <i>ERMAP</i> alleles encoding Scianna (SC) antigens

Srivastava, Kshitij; Lee, Eunah; Owens, Eric A.; Rujirojindakul, Pairaya; Flegel, Willy A.

doi:10.1111/trf.13801

Cited by 11 publications

(22 citation statements)

References 29 publications

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“…The sequence information for 48 ERMAP alleles was retrieved from GenBank (KX265189–KX265236) [21]. The phylogenetic tree was rooted using the chimpanzee ERMAP sequence as outgroup (GenBank number NC_006468.4; range 42,268,258 to 42,295,767).…”

Section: Methodsmentioning

confidence: 99%

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The phylogeny of 48 alleles, experimentally verified at 21 kb, and its application to clinical allele detection

Srivastava¹,

Wollenberg²,

Flegel³

2019

J Transl Med

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BackgroundSequence information generated from next generation sequencing is often computationally phased using haplotype-phasing algorithms. Utilizing experimentally derived allele or haplotype information improves this prediction, as routinely used in HLA typing. We recently established a large dataset of long ERMAP alleles, which code for protein variants in the Scianna blood group system. We propose the phylogeny of this set of 48 alleles and identify evolutionary steps to derive the observed alleles.MethodsThe nucleotide sequence of > 21 kb each was used for all physically confirmed 48 ERMAP alleles that we previously published. Full-length sequences were aligned and variant sites were extracted manually. The Bayesian coalescent algorithm implemented in BEAST v1.8.3 was used to estimate a coalescent phylogeny for these variants and the allelic ancestral states at the internal nodes of the phylogeny.ResultsThe phylogenetic analysis allowed us to identify the evolutionary relationships among the 48 ERMAP alleles, predict 4243 potential ancestral alleles and calculate a posterior probability for each of these unobserved alleles. Some of them coincide with observed alleles that are extant in the population.ConclusionsOur proposed strategy places known alleles in a phylogenetic framework, allowing us to describe as-yet-undiscovered alleles. In this new approach, which relies heavily on the accuracy of the alleles used for the phylogenetic analysis, an expanded set of predicted alleles can be used to infer alleles when large genotype data are analyzed, as typically generated by high-throughput sequencing. The alleles identified by studies like ours may be utilized in designing of microarray technologies, imputing of genotypes and mapping of next generation sequencing data.Electronic supplementary materialThe online version of this article (10.1186/s12967-019-1791-9) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

“…We have previously assessed the nucleotide variations in the ERMAP gene and unambiguously identified 48 alleles at 21,406 nucleotides each in 50 unrelated individuals from 5 different populations [21]. We propose using the phylogeny of this set of 48 alleles and identifying evolutionary steps to derive the observed alleles [22].…”

Section: Introductionmentioning

confidence: 99%

The phylogeny of 48 alleles, experimentally verified at 21 kb, and its application to clinical allele detection

Srivastava¹,

Wollenberg²,

Flegel³

2019

J Transl Med

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“…Heterozygosity at a single site or complete homozygosity allowed for the unambiguous assignment of a haplotype as described previously 33 . Allele-specific PCR and subsequent sequencing of the PCR products were used to construct the haplotype structure in samples with more than one heterozygous site.…”

Section: Methodsmentioning

confidence: 99%

Long-range haplotype analysis of the malaria parasite receptor gene ACKR1 in an East-African population

et al. 2018

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The human ACKR1 gene encodes a glycoprotein expressing the Duffy blood group antigens (Fy). The Duffy protein acts as a receptor for distinct pro-inflammatory cytokines and malaria parasites. We determined the haplotypes of the ACKR1 gene in a population inhabiting a malaria-endemic area. We collected blood samples from 60 healthy volunteers in Ethiopia’s southwestern low-altitude tropical region. An assay was devised to amplify the ACKR1 gene as a single amplicon and determine its genomic sequence. All haplotypes were resolved at 5178 nucleotides each, covering the coding sequence (CDS) of the ACKR1 gene and including the 5′- and 3′-untranslated regions (UTR), intron 1, and the 5′- and 3′-flanking regions. When necessary, allele-specific PCR with nucleotide sequencing or length polymorphism analysis was applied. Among the 120 chromosomes analyzed, 18 ACKR1 alleles were confirmed without ambiguity. We found 18 single-nucleotide polymorphisms (SNPs); only one SNP was novel. The non-coding sequences harbored 14 SNPs. No SNP, other than c.-67T>C, indicative of a non-functional allele, was detected. We described haplotypes of the ACKR1 gene in an autochthonous East-African population and found 18 distinct ACKR1 alleles. These long-range alleles are useful as templates to phase and analyze next-generation sequencing data, thus enhancing the reliability of clinical diagnostics.

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“…The Scianna system is now composed of seven antigens: a pair of antithetical antigens (the high‐ and low‐frequency, Sc1 and Sc2), an antigen of low frequency (Sc4), and four antigens of very high frequency (Sc3, Sc5, Sc6, and Sc7) . Scianna antigens are located on the immunoglobulin‐superfamily glycoprotein ERMAP (for erythroblast membrane‐associated protein), and studies have shown that the ERMAP gene is located on chromosome 1p, adjacent to the Rh genes . Scianna antigens are well developed at birth and expressed on cord RBCs…”

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“…5,6 Scianna antigens are located on the immunoglobulin-superfamily glycoprotein ERMAP (for erythroblast membrane-associated protein), and studies have shown that the ERMAP gene is located on chromosome 1p, adjacent to the Rh genes. [5][6][7] Scianna antigens are well developed at birth and expressed on cord RBCs. 5 Sc1 incidence is more than 99% in all populations while only approximately 1% of people of European ancestry, mainly Mennonites, express Sc2.…”

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The first case of severe acute hemolytic transfusion reaction caused by anti‐Sc2

et al. 2018

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BACKGROUND Alloantibodies to the low‐frequency antigen Scianna‐2 (Sc2) have been implicated in cases of hemolytic disease of the fetus and newborn but never in hemolytic transfusion reactions (HTRs); thus, the clinical significance of anti‐Sc2 has yet to be fully addressed. STUDY DESIGN AND METHODS A 26‐year‐old woman with thalassemia presented rigors, fever, nausea, abdominal pain, and hemolytic biochemistry after exposure to 75 mL of plasma‐reduced red blood cells (RBCs). The RBC unit was issued by electronic crossmatch but was 3+ incompatible on recrossmatch by gel indirect antiglobulin test (IAT). The patient had anti‐Sc2 previously identified, but considered to be clinically insignificant. The transfusion history was reviewed and a monocyte monolayer assay (MMA) was performed. RESULTS The patient was investigated for a RBC reaction 9 years prior, when she developed symptoms of HTR. The RBC unit was crossmatched by immediate spin due to consistent screen negativity. Full crossmatch found the RBC 1+ incompatible by gel IAT with both pre/post samples, while direct antiglobulin test was negative (pre) and 1+ immunoglobulin G positive (post). The antibody remained unidentified and she was committed to gel IAT crossmatch. Two‐years later, the specificity to Sc2 was deduced when one RBC unit was found 3+ incompatible. Finally, the transfusion reaction reported herein occurred when she received by happenstance RBCs from the same donor who was associated with the remote reaction 9 years earlier. MMA yielded highly positive phagocytic indices only for Sc2+ RBCs, including the donor's RBCs that triggered the severe HTR. CONCLUSION This is the first case of HTR caused by anti‐Sc2 confirmed by clinical findings and MMA.

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Full‐length nucleotide sequence of ERMAP alleles encoding Scianna (SC) antigens

Cited by 11 publications

References 29 publications

The phylogeny of 48 alleles, experimentally verified at 21 kb, and its application to clinical allele detection

The phylogeny of 48 alleles, experimentally verified at 21 kb, and its application to clinical allele detection

Long-range haplotype analysis of the malaria parasite receptor gene ACKR1 in an East-African population

The first case of severe acute hemolytic transfusion reaction caused by anti‐Sc2

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