The experience of extended blood group genotyping by next‐generation sequencing (NGS): investigation of patients with sickle‐cell disease

Fichou, Yann; Mariez, M.; Maréchal, Cédric Le; Férec, Claude

doi:10.1111/vox.12432

Cited by 39 publications

(41 citation statements)

References 33 publications

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“…Distinguishing neutral passenger variants from deleterious mutations has challenged genomics from its inception, and as NGS is applied to transfusion medicine, novel blood group variants have been a recurrent finding . Several prediction tools used widely in genomics have not been tested for immunohematology.…”

Section: Discussionmentioning

confidence: 99%

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Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 Genomes Project

et al. 2018

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BACKGROUND The 1000 Genomes Project provides a database of genomic variants from whole genome sequencing of 2504 individuals across five continental superpopulations. This database can enrich our background knowledge of worldwide blood group variant geographic distribution and identify novel variants of potential clinical significance. STUDY DESIGN AND METHODS The 1000 Genomes database was analyzed to 1) expand knowledge about continental distributions of known blood group variants, 2) identify novel variants with antigenic potential and their geographic association, and 3) establish a baseline scaffold of chromosomal coordinates to translate next‐generation sequencing output files into a predicted red blood cell (RBC) phenotype. RESULTS Forty‐two genes were investigated. A total of 604 known variants were mapped to the GRCh37 assembly; 120 of these were reported by 1000 Genomes in at least one superpopulation. All queried variants, including the ACKR1 promoter silencing mutation, are located within exon pull‐down boundaries. The analysis yielded 41 novel population distributions for 34 known variants, as well as 12 novel blood group variants that warrant further validation and study. Four prediction algorithms collectively flagged 79 of 109 (72%) known antigenic or enzymatically detrimental blood group variants, while 4 of 12 variants that do not result in an altered RBC phenotype were flagged as deleterious. CONCLUSION Next‐generation sequencing has known potential for high‐throughput and extended RBC phenotype prediction; a database of GRCh37 and GRCh38 chromosomal coordinates for 120 worldwide blood group variants is provided as a basis for this clinical application.

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Section: Discussionmentioning

confidence: 99%

“…A number of successful clinical applications have been reported, and further efforts are under way in the areas of oncology, hemostasis, obstetrics, and pharmacology to identify the clinical benefits of genomic medicine . Transfusion medicine is an additional discipline with a strong genetics foundation that is exploring this approach …”

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confidence: 99%

Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 Genomes Project

et al. 2018

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“…The inherent “personalized” nature of selecting the best blood product for each patient, along with the breadth of genomic information potentially relevant for transfusion therapy (e.g., red blood cells [RBCs], platelets [PLTs], neutrophil antigens, and HLA) and the documented clinical value, make transfusion medicine an ideal field for the use of NGS or MPS data. A number of publications over the past 6 years have provided sound proof‐of‐principle examples of the application of targeted (sequencing specific genes), exome (sequencing the coding regions only), or whole genome (sequencing both coding and noncoding regions) NGS to determine the extended RBC, PLT, RH, or HLA profiles of patients or donors …”

Section: Ngs or Mps Approachesmentioning

confidence: 99%

The “next generation” reference laboratory?

Montemayor‐Garcia

Westhoff

2018

Transfusion

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“…A recent proof‐of‐principle study demonstrated the capability of using whole genome sequencing data for comprehensive antigen prediction of RBCs and platelets . A targeted exome sequencing approach has been recognized for its utility in blood group genotyping and has been predicted to facilitate investigation of novel blood group alleles . While studies have shown proof of principle for blood group genotyping by MPS, no studies have investigated to date its clinical application to resolve complex cases in a reference laboratory setting …”

mentioning

confidence: 99%

Targeted exome sequencing defines novel and rare variants in complex blood group serology cases for a red blood cell reference laboratory setting

et al. 2017

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Targeted exome sequencing resolved complex serology problems and defined both novel blood group alleles (CD55:c.203G>A, ABCB6:c.1118_1124delCGGATCG, ABCB6:c.1656-1G>A, and RHD:c.452G>A) and rare variants on blood group alleles associated with altered phenotypes. This study illustrates the utility of exome sequencing, in conjunction with serology, as an alternative approach to resolve complex cases.

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The experience of extended blood group genotyping by next‐generation sequencing (NGS): investigation of patients with sickle‐cell disease

Cited by 39 publications

References 33 publications

Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 Genomes Project

Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 Genomes Project

The “next generation” reference laboratory?

Targeted exome sequencing defines novel and rare variants in complex blood group serology cases for a red blood cell reference laboratory setting

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