BACKGROUND: Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. STUDY DESIGN AND METHODS: Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform. Genes for 28 protein-based blood group systems, GATA1, and KLF1 were analyzed. Copy number variation analysis was used to characterize complex structural variants in the GYPC and RH systems. RESULTS: The average sequencing depth per target region was 66.2 ± 39.8. Each sample harbored on average 43 ± 9 variants, of which 10 ± 3 were used for genotyping. For the 28 samples, massively parallel sequencing variant sequences correctly matched expected sequences based on single nucleotide polymorphism genotyping data. Copy number variation analysis defined the Rh C/c alleles and complex RHD hybrids. Hybrid RHD*D-CE-D variants were correctly identified, but copy number variation analysis did not confidently distinguish between D and CE exon deletion versus rearrangement. CONCLUSION: The targeted exome sequencing strategy employed extended the range of blood group genotypes detected compared with single nucleotide polymorphism typing. This single-test format included detection of complex MNS hybrid cases and, with copy number variation analysis, defined RH hybrid genes along with the RHCE*C allele hitherto difficult to resolve by variant detection. The approach is economical compared with whole-genome sequencing and is suitable for a red blood cell reference laboratory setting.
BACKGROUND: Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. STUDY DESIGN AND METHODS: Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform. Genes for 28 protein-based blood group systems, GATA1, and KLF1 were analyzed. Copy number variation analysis was used to characterize complex structural variants in the GYPC and RH systems. RESULTS: The average sequencing depth per target region was 66.2 ± 39.8. Each sample harbored on average 43 ± 9 variants, of which 10 ± 3 were used for genotyping. For the 28 samples, massively parallel sequencing variant sequences correctly matched expected sequences based on single nucleotide polymorphism genotyping data. Copy number variation analysis defined the Rh C/c alleles and complex RHD hybrids. Hybrid RHD*D-CE-D variants were correctly identified, but copy number variation analysis did not confidently distinguish between D and CE exon deletion versus rearrangement. CONCLUSION: The targeted exome sequencing strategy employed extended the range of blood group genotypes detected compared with single nucleotide polymorphism typing. This single-test format included detection of complex MNS hybrid cases and, with copy number variation analysis, defined RH hybrid genes along with the RHCE*C allele hitherto difficult to resolve by variant detection. The approach is economical compared with whole-genome sequencing and is suitable for a red blood cell reference laboratory setting.
Authors: Huagang Hou; Jin H Baek; Hao Zhang; Francine Wood; Yamei Gao; Ann B Flood; Harold M Swartz; Paul W Buehler Journal: Blood Transfus Date: 2019-05-16 Impact factor: 3.443
Authors: Celina Montemayor-Garcia; Panagiota Karagianni; David A Stiles; Erika M Reese; Danielle A Smellie; Debrean A Loy; Kimberly Y Levy; Magdalene Nwokocha; Marina U Bueno; Jeffery L Miller; Harvey G Klein Journal: Transfusion Date: 2018-10-12 Impact factor: 3.157
Authors: Genghis H Lopez; Brett Wilson; Robyn M Turner; Glenda M Millard; Nicole S Fraser; Naomi M Roots; Yew-Wah Liew; Catherine A Hyland; Robert L Flower Journal: Transfus Med Hemother Date: 2019-11-14 Impact factor: 3.747
Authors: Ti-Cheng Chang; Kelly M Haupfear; Jing Yu; Evadnie Rampersaud; Vivien A Sheehan; Jonathan M Flanagan; Jane S Hankins; Mitchell J Weiss; Gang Wu; Sunitha Vege; Connie M Westhoff; Stella T Chou; Yan Zheng Journal: Blood Adv Date: 2020-09-22
Authors: Stella T Chou; Jonathan M Flanagan; Sunitha Vege; Naomi L C Luban; R Clark Brown; Russell E Ware; Connie M Westhoff Journal: Blood Adv Date: 2017-08-03