N. Rachel, K. M. Kennedy, A. Suleiman, K. Christine, Chege Evelynn, Obiero Celestino, H. L. Genghis, V. R. Eileen, A. Catherine, L. F. Robert
A variant is an alternative nucleotide located at a specific region of a gene. 48 genes encode for human red cell blood group systems. Variants within these genes encode for alleles, which can be highly polymorphic. The blood group gene loci jointly display all types of inherited variants to include single nucleotide variants (SNVs), insertions/deletions (indels), and structural variants. In Africa, there is limited information on the red cell variants. The aim of the study was to determine the incidence of Kell red blood cell variants among the Kenyans. Blood donor’s samples that were used for routine grouping process were identified for this study. Next generation sequencing method was employed to predict the Kell red cell variants in blood donor samples. Descriptive statistics was applied and the result was presented in form of tables. The study reveals that Kell system has six variants with two major phenotypes and genotpes. The most common phenotype genotyped was KEL2 (KEL*02/KEL*02) 79% (85/108) followed by KEL2 KEL6 KEL7 (KEL*02.06/KEL*02) 16.7% (18/108). The rest were found to be of low frequency and all were associated with KEL2. The study recommends an extended study with a large sample size and introduction of extended phenotyping to aid Kell antigens identification in the donor population.
{"title":"Molecular organisation of Kell (KEL) red blood cell variants among voluntary blood donors at the National Blood Grouping Testing Laboratory, Kenya","authors":"N. Rachel, K. M. Kennedy, A. Suleiman, K. Christine, Chege Evelynn, Obiero Celestino, H. L. Genghis, V. R. Eileen, A. Catherine, L. F. Robert","doi":"10.5897/jbsa2022.0117","DOIUrl":"https://doi.org/10.5897/jbsa2022.0117","url":null,"abstract":"A variant is an alternative nucleotide located at a specific region of a gene. 48 genes encode for human red cell blood group systems. Variants within these genes encode for alleles, which can be highly polymorphic. The blood group gene loci jointly display all types of inherited variants to include single nucleotide variants (SNVs), insertions/deletions (indels), and structural variants. In Africa, there is limited information on the red cell variants. The aim of the study was to determine the incidence of Kell red blood cell variants among the Kenyans. Blood donor’s samples that were used for routine grouping process were identified for this study. Next generation sequencing method was employed to predict the Kell red cell variants in blood donor samples. Descriptive statistics was applied and the result was presented in form of tables. The study reveals that Kell system has six variants with two major phenotypes and genotpes. The most common phenotype genotyped was KEL2 (KEL*02/KEL*02) 79% (85/108) followed by KEL2 KEL6 KEL7 (KEL*02.06/KEL*02) 16.7% (18/108). The rest were found to be of low frequency and all were associated with KEL2. The study recommends an extended study with a large sample size and introduction of extended phenotyping to aid Kell antigens identification in the donor population.","PeriodicalId":405477,"journal":{"name":"Journal of Bioinformatics and Sequence Analysis","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126653209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N. Rachel, K. M. Kennedy, A. Suleiman, K. Christine, Chege Evelynn, Obiero Celestino, H. L. Genghis, V. R. Eileen, A. Catherine, L. F. Robert
A variant is an alternative nucleotide located at a specific region of a gene. 48 genes encode for human red cell blood group systems. Variants within these genes encode for alleles, which can be highly polymorphic. The blood group gene loci jointly display all types of inherited variants to include single nucleotide variants insertions/deletions and structural variants. In Africa, there is limited information on the red cell variants. The aim of the study was to establish the frequency Duffy red blood cell variants among the donors in Kenya. The study employed next sequencing method, descriptive statistics and results presented in form of a table. The findings show that Duffy system has three variants to include; homozygous for FY*Null GATA regulatory box variant FY*02N.01/FY*02N.01 or Fy(a–b–) found in 93.52% (101/108), while FY*01/FY*02 and FY c.–67T>C predicted Fy(a+b–) or Fy(a–b+) at 3.70% (4/108) while FY*02/FY*02N.01 predicted Fy(a–b+) at 2.78% (3/108). This study recommends an extended research involving large sample size and introduction of extended phenotyping in the identification of FY antigens population.
{"title":"Molecular characterisation of Duffy (FY) red blood cell variants among voluntary blood donors at the National Blood Grouping Testing Laboratory, Kenya","authors":"N. Rachel, K. M. Kennedy, A. Suleiman, K. Christine, Chege Evelynn, Obiero Celestino, H. L. Genghis, V. R. Eileen, A. Catherine, L. F. Robert","doi":"10.5897/jbsa2022.0116","DOIUrl":"https://doi.org/10.5897/jbsa2022.0116","url":null,"abstract":"A variant is an alternative nucleotide located at a specific region of a gene. 48 genes encode for human red cell blood group systems. Variants within these genes encode for alleles, which can be highly polymorphic. The blood group gene loci jointly display all types of inherited variants to include single nucleotide variants insertions/deletions and structural variants. In Africa, there is limited information on the red cell variants. The aim of the study was to establish the frequency Duffy red blood cell variants among the donors in Kenya. The study employed next sequencing method, descriptive statistics and results presented in form of a table. The findings show that Duffy system has three variants to include; homozygous for FY*Null GATA regulatory box variant FY*02N.01/FY*02N.01 or Fy(a–b–) found in 93.52% (101/108), while FY*01/FY*02 and FY c.–67T>C predicted Fy(a+b–) or Fy(a–b+) at 3.70% (4/108) while FY*02/FY*02N.01 predicted Fy(a–b+) at 2.78% (3/108). This study recommends an extended research involving large sample size and introduction of extended phenotyping in the identification of FY antigens population.","PeriodicalId":405477,"journal":{"name":"Journal of Bioinformatics and Sequence Analysis","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115711497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Providence virus is the only member of the family Carmotetraviridae and carries a positive single stranded RNA genome that encodes three open reading frames. The smallest open reading frame encodes the structural proteins. The largest open reading frame encodes a large putative protein, p130. The second overlapping open reading frame encodes two non-structural proteins; p40, a proposed accessory protein and p104, the replicase, containing the RdRp domain. Till date, p130 and p40 are not associated with any related open reading frames in the databases. The purpose of this study is to identify sequences within these non-structural proteins with potential roles in replication and evolution using computational tools. Our results revealed that p130 has a putative arginine-rich sequence which lies in the disordered region also found in the Umbravirus, Groundnut rosette virus p27. Analysis of the p40 revealed a sequence with a coiled-coil conformation and surface-exposed characteristics comparable to the interaction domain of Tombusvirus, Tomato bushy stunt virus p33 accessory protein. The hypothetical two transmembrane helix topology of PrV p104 oriented the putative localization signal at the N-terminus, the same way the localization signal of Tomato bushy stunt virus p92 is oriented. This study concluded that Providence virus non-structural proteins are structurally related to Tombusvirus and Umbravirus accessory proteins and contain sequences with predicted functions in replication. Findings from this study have led us to propose a co-evolutionary event between an insect and plant virus resulting in a hybrid virus with the potential to infect and replicate in both host plant and animal systems. Key words: Providence virus, non-structural proteins, p40, p130, sequence comparison, replication, evolution.
{"title":"Computational characterization of providence virus non-structural proteins: Evolutionary and functional implications","authors":"Nakayinga Ritah","doi":"10.5897/JBSA2019.0111","DOIUrl":"https://doi.org/10.5897/JBSA2019.0111","url":null,"abstract":"Providence virus is the only member of the family Carmotetraviridae and carries a positive single stranded RNA genome that encodes three open reading frames. The smallest open reading frame encodes the structural proteins. The largest open reading frame encodes a large putative protein, p130. The second overlapping open reading frame encodes two non-structural proteins; p40, a proposed accessory protein and p104, the replicase, containing the RdRp domain. Till date, p130 and p40 are not associated with any related open reading frames in the databases. The purpose of this study is to identify sequences within these non-structural proteins with potential roles in replication and evolution using computational tools. Our results revealed that p130 has a putative arginine-rich sequence which lies in the disordered region also found in the Umbravirus, Groundnut rosette virus p27. Analysis of the p40 revealed a sequence with a coiled-coil conformation and surface-exposed characteristics comparable to the interaction domain of Tombusvirus, Tomato bushy stunt virus p33 accessory protein. The hypothetical two transmembrane helix topology of PrV p104 oriented the putative localization signal at the N-terminus, the same way the localization signal of Tomato bushy stunt virus p92 is oriented. This study concluded that Providence virus non-structural proteins are structurally related to Tombusvirus and Umbravirus accessory proteins and contain sequences with predicted functions in replication. Findings from this study have led us to propose a co-evolutionary event between an insect and plant virus resulting in a hybrid virus with the potential to infect and replicate in both host plant and animal systems. \u0000 \u0000 Key words: Providence virus, non-structural proteins, p40, p130, sequence comparison, replication, evolution.","PeriodicalId":405477,"journal":{"name":"Journal of Bioinformatics and Sequence Analysis","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122398169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oligonucleotide microarrays data pre-processing procedures impacting gene expression differential survey performances were fully evoked. RNA-Seq tool exhibited high performances (sensitivity) as opposed to microarrays in transcriptomic as well as genomic studies. The aim of this study is to evaluate microarrays data pre-processing dynamism on gene expression differential analysis outcomes, assuming RNA-Seq approach as reference. For this purpose, significantly differentially expressed genes (DEGs) candidate by processing two Vitis vinifera development stages (veraison and repining), from previous comparative transcriptomic analysis, between RNA-Seq and our own developed custom microarrays designs submitted to 20 different data pre-processing procedures combination schemes in terms of expressed genes signal normalization (DN) and background subtraction (BS) functions developed in R limma package, were structured in nine (9) blocks, depending on microarrays DN+BS and as well BS+DN arrangements, and considered for multivariate statistical analysis. In total, 17,446 genes were common across all microarrays by processing the above mentioned V. vinifera differential analysis and were detected for the subsequent survey. Findings, although recognizing data pre-processing practices as a necessary step for improving microarrays performances suggested background correction procedure (BS+DN) as promoting DEGs data variability by contrast to genes signal normalization pattern (DN+BS). Also, results revealed DN+BS microarray data pre-processing procedure as enhancing oligonucleotide microarrays positive predictive value as well as sensitivity performances. In conclusion, the present survey highlighted the strong impact of microarray data pre-processing procedures (BS+DN and/or DN+BS) on gene expression differential analysis outcome and as well confirmed RNA-Seq as an acceptable approach in assessing oligonucleotide microarray performances in transcriptomic surveys. Key words: Microarrays, RNA-Seq, Background subtraction (BS), expressed genes signal normalization (DN), Differential analysis, Vitis vinifera.
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