A DEL phenotype attributed to <i>RHD</i> Exon 9 sequence deletion: slipped‐strand mispairing and blood group polymorphisms

Lopez, Genghis H.; Turner, Robyn; McGowan, Eunike C.; Schoeman, Elizna M.; Scott, Stacy A.; O’Brien, Helen; Millard, Glenda; Roulis, Eileen; Allen, Amanda J; Liew, Yew‐Wah; Flower, Robert L.; Hyland, Catherine A.

doi:10.1111/trf.14439

Cited by 9 publications

(4 citation statements)

References 36 publications

(110 reference statements)

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“…Meanwhile, long-range PCR applications for RHD have been described and studies for the FY (Duffy) alleles were described above (Halawani et al, 2014;Lopez et al, 2018;Yin et al, 2018). A recent study describes an important advance whereby the complete RHD sequence was provided using MPS technology (Tounsi et al, 2018).…”

Section: Current Challenges With Mps "Read Lengths" and Defining Refementioning

confidence: 99%

Developments beyond blood group serology in the genomics era

2019

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Summary Blood group serology and single nucleotide polymorphism‐based genotyping platforms are accurate but do not provide a comprehensive cover for all 36 blood group systems and do not cover the antigen diversity observed among population groups. This review examines the extent to which genomics is shaping blood group serology. Resources for genomics include the Human Reference Genome Sequence assembly; curated blood group tables listing variants; public databases providing information on genetic variants from world‐wide studies; and massively parallel sequencing technologies. Blood group genomic studies span the spectrum, from bioinformatic data mining of huge data sets containing whole genome and whole exome information to laboratory investigations utilising targeted sequencing approaches. Blood group predictions based on genome sequencing and genomic studies are proving accurate, and have shown utility in both research and reference settings. Overall, studies confirm the potential for blood group genomics to reshape donor and patient transfusion management strategies to provide more compatible blood transfusions.

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Section: Current Challenges With Mps "Read Lengths" and Defining Refementioning

confidence: 99%

Developments beyond blood group serology in the genomics era

2019

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“…False results are also reported when SNV occurs next to the tested region and affects the expression. [42][43][44] The software used for the interpretation of results requires regular updating to be compatible with the updated allelic databases, but even then it is impossible to test all the known alternations.…”

Section: Blood Group Genotypingmentioning

confidence: 99%

<p>Potential of next-generation sequencing to match blood group antigens for transfusion</p>

Orzińska¹,

Guz²,

Brojer³

2019

IJCTM

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A review of the advances in applying next-generation sequencing (NGS) to transfusion medicine for the purpose of genotyping alleles encoding clinically important red blood cell and platelet antigens. NGS data from published studies confirm the possibility of antigen prediction based on sequencing of the whole genome, exome or targeted regions. What remains a challenge, to provide highly accurate NGS genotyping, is the further improvement of bioinformatic solutions for automated interpretation based on publicly accessible and improved reference databases appropriate for NGS methods as well as validation of a method based on the examination of a large number of individuals. There is no doubt, however, as to the future of NGS as a supplementary test used to provide highly compatible blood as well as to reduce the risk of patient's alloimmunization. This is part of personalized medicine.

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“…Specifically, RHD*01N.67 which includes exon 1, 1,2 RHD*Ex2del which includes exon 2 3 (this deletion appears uncertain, given the methods used and the publication referenced within), RHD*Ex3del,602G,667G,819A which includes exon 3, 4 RHD*DEL30/RHD*01EL.30 which includes exon 8, 5 RHD*Ex9del which includes exon 9, 6 and RHD*Ex10del type1, RHD*Ex10del type2 both of which include exon 10. 1,7 The breakpoints of these alleles have been characterized to various extents (fully in Refs., 1,[4][5][6][7] partially in Ref., 2 uncharacterized in Ref. 3 ).…”

Section: Introductionmentioning

confidence: 99%

Two new RHD alleles with deletions spanning multiple exons

et al. 2020

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Background: The most common large-deletion RHD allele (RHD*01N.01) includes the entire coding sequence, intervening regions and untranslated regions. The rest of large-deletion RHD alleles reported to-date consist of single-exon deletions, such as RHD*01N.67 which includes exon 1. Materials and Methods: Samples from two donors with RhD-negative serology yielded unclear or inconclusive results when subject to confirmatory testing on RHD genotyping arrays. To determine their RHD genotypes, genomic DNA was analyzed with a combination of allele-specific PCR, long-range PCR, Sanger sequencing, and next-generation sequencing assays. Results: Allele-specific PCR failed to detect products for RHD exons 1 to 3 in one sample and RHD exons 1 to 5 in the other. A quantitative next-generation sequencing assay confirmed deletion of exons 1 to 3 and 1 to 5 respectively, and detected the absence of an RHD gene in trans in both samples. Long-range PCR and Sanger sequencing enabled identification of the breakpoints for both alleles. Both deletions start within the 5 0 Rhesus box (upstream of the identity region for the 1-to-3 deletion, downstream of it for the 1-to-5 deletion), and end within introns. Conclusions: Resolution of unclear or inconclusive results from targeted genotyping arrays often leads to the discovery of new alleles. The 5 0 Rhesus box may be a hot spot for genetic recombination events, such as the large deletions described in this report.

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A DEL phenotype attributed to RHD Exon 9 sequence deletion: slipped‐strand mispairing and blood group polymorphisms

Cited by 9 publications

References 36 publications

Developments beyond blood group serology in the genomics era

Developments beyond blood group serology in the genomics era

<p>Potential of next-generation sequencing to match blood group antigens for transfusion</p>

Two new RHD alleles with deletions spanning multiple exons

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