1
|
Liu Z, Liu M, Mercado T, Illoh O, Davey R. Extended blood group molecular typing and next-generation sequencing. Transfus Med Rev 2014; 28:177-86. [PMID: 25280589 DOI: 10.1016/j.tmrv.2014.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 08/11/2014] [Accepted: 08/25/2014] [Indexed: 02/09/2023]
Abstract
Several high-throughput multiplex blood group molecular typing platforms have been developed to predict blood group antigen phenotypes. These molecular systems support extended donor/patient matching by detecting commonly encountered blood group polymorphisms as well as rare alleles that determine the expression of blood group antigens. Extended molecular typing of a large number of blood donors by high-throughput platforms can increase the likelihood of identifying donor red blood cells that match those of recipients. This is especially important in the management of multiply-transfused patients who may have developed several alloantibodies. Nevertheless, current molecular techniques have limitations. For example, they detect only predefined genetic variants. In contrast, target enrichment next-generation sequencing (NGS) is an emerging technology that provides comprehensive sequence information, focusing on specified genomic regions. Target enrichment NGS is able to assess genetic variations that cannot be achieved by traditional Sanger sequencing or other genotyping platforms. Target enrichment NGS has been used to detect both known and de novo genetic polymorphisms, including single-nucleotide polymorphisms, indels (insertions/deletions), and structural variations. This review discusses the methodology, advantages, and limitations of the current blood group genotyping techniques and describes various target enrichment NGS approaches that can be used to develop an extended blood group genotyping assay system.
Collapse
Affiliation(s)
- Zhugong Liu
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD.
| | - Meihong Liu
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
| | - Teresita Mercado
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
| | - Orieji Illoh
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
| | - Richard Davey
- Division of Blood Components and Devices, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD
| |
Collapse
|
2
|
Black HA, Khan FF, Tyson J, Armour JAL. Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus. BMC Genomics 2014; 15:614. [PMID: 25048054 PMCID: PMC4117965 DOI: 10.1186/1471-2164-15-614] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/14/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3-16); hence, the mechanisms responsible for changes in copy number at this locus are unclear. RESULTS In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure. CONCLUSIONS Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.
Collapse
Affiliation(s)
- Holly A Black
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH UK
| | - Fayeza F Khan
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH UK
| | - Jess Tyson
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH UK
| | - John AL Armour
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH UK
| |
Collapse
|
3
|
Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin SH. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science 2013; 342:253-7. [PMID: 24115442 PMCID: PMC4018826 DOI: 10.1126/science.1242088] [Citation(s) in RCA: 460] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies (GWASs) have ascertained numerous trait-associated common genetic variants, frequently localized to regulatory DNA. We found that common genetic variation at BCL11A associated with fetal hemoglobin (HbF) level lies in noncoding sequences decorated by an erythroid enhancer chromatin signature. Fine-mapping uncovers a motif-disrupting common variant associated with reduced transcription factor (TF) binding, modestly diminished BCL11A expression, and elevated HbF. The surrounding sequences function in vivo as a developmental stage-specific, lineage-restricted enhancer. Genome engineering reveals the enhancer is required in erythroid but not B-lymphoid cells for BCL11A expression. These findings illustrate how GWASs may expose functional variants of modest impact within causal elements essential for appropriate gene expression. We propose the GWAS-marked BCL11A enhancer represents an attractive target for therapeutic genome engineering for the β-hemoglobinopathies.
Collapse
Affiliation(s)
- Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
- Harvard Medical School, Boston, MA, 02115
| | - Sophia C. Kamran
- Harvard Medical School, Boston, MA, 02115
- Howard Hughes Medical Institute, Boston, MA, 02115
| | - Samuel Lessard
- Montreal Heart Institute and Université Montréal, Montreal, Quebec, H1T 1C8, Canada
| | - Jian Xu
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
- Harvard Medical School, Boston, MA, 02115
| | - Yuko Fujiwara
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
| | - Carrie Lin
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
| | - Zhen Shao
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
| | | | - Elenoe C. Smith
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
| | - Luca Pinello
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115
| | - Peter J. Sabo
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, 98195
| | - Jeff Vierstra
- Departments of Genome Sciences and Medicine, University of Washington, Seattle, WA, 98195
| | - Richard A. Voit
- Department of Pediatrics, Stanford University, Palo Alto, CA, 94304
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115
- Harvard School of Public Health, Boston, MA, 02115
| | | | | | - Guillaume Lettre
- Montreal Heart Institute and Université Montréal, Montreal, Quebec, H1T 1C8, Canada
| | - Stuart H. Orkin
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, 02115
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115
- Harvard Medical School, Boston, MA, 02115
- Howard Hughes Medical Institute, Boston, MA, 02115
| |
Collapse
|