Quality and Quantity of Nucleic Acids Extracted from Formalin-Fixed Paraffin-Embedded Lymphoma Biopsies from Nigerian Archived Biopsy.

BACKGROUND: Integrity of nucleic acids derived from archived formalin-fixed paraffin-embedded (FFPE) cancer specimens affects diagnosis, prognosis, and therapy. Several factors affect the quality and quantity of extracted nucleic acids and one of such factors is storage period. AIM: We investigated the impact of storage duration on the quality and quantity of nucleic acids extracted from archived FFPE lymphoma biopsies in Nigeria. MATERIALS AND METHODS: A total of 53 FFPE biopsies diagnosed as lymphoma stored over several years (2008-2019) were analyzed. They were 22 chronic lymphocytic leukemia (CLL) cases, 17 Hodgkin lymphoma (HL) cases, and 14 diffuse large B-cell lymphoma, not otherwise specified (DLBCL, NOS). DNA was extracted from all the lymphoma samples which were analyzed for integrity and amplifiability using the four pairs of control genes polymerase chain reaction (PCR) primers of BIOMED-2 protocol, whereas RNA extraction was from 6 CLL cases used for qPCR analysis of RNU43. RESULTS: For CLL, the mean DNA yield was 193.6 ng/µl (range: 3.0-533.0 ng/µl), whereas the mean A260/A280 ratio was 1.7 (1.2-1.9). For DLBCL, NOS, and HL, 255.5 ng/µl (range: 32.9-605.4 ng/µl), 1.8 (1.5-2.0) and 242.7 ng/µl (range: 1.3-886.0 ng/µl), and 1.7 (0.9-1.8), respectively. The extracted DNA gave amplifiable products of at least 200bp, whereas the RNA analysis showed CT values of <38 in all the samples. The mean RNA yield was 462.2 ng/µl (range: 74.7-1082.1), whereas the mean A260/A280 was 1.7 (1.5-1.8). CONCLUSION: Quantity and quality of nucleic acids from FFPE tissues stored for different time periods showed no significant difference in yield and quality.

Assessment of MTR Rs1805087 SNP as Possible Modifier of Sickle Cell Disease Severity in a Nigerian Population.

BACKGROUND: Sickle cell disease is the commonest genetic disorder in Nigeria, affecting 2-3% of an estimated population of 160 million people. The role of genetic mutations in folate cycle genes, and the variable phenotypic expressions constituting disease severity, needs to be critically examined. OBJECTIVE: This study was carried out to establish the pattern of methionine synthase gene mutations (rs1805087 SNP), and its possible association with disease severity in adults with sickle cell anaemia in Lagos, Nigeria. METHODOLOGY: This is a cross-sectional study of seventy (70) subjects with sickle cell disease (HbSS) matched for age and gender with known apparently healthy haemoglobin genotype AA (HbAA) subjects, as cases and controls respectively. Structured questionnaires were used to obtain demographic, clinical and other phenotypic data needed to compute disease severity. Pattern of MTR A2756G gene mutation and homocysteine assay (Hcy) were assessed by Polymerase Chain Reaction and Enzyme- linked Immunosorbent Assay respectively. Full blood count analysis of participants was done using the KX-21 Automated Analyzer (Sysmex Corporation, Japan). RESULTS: The mutant genotypes MTR 2756 AG/GG were recorded in 46.4% (n =55) of subjects with disease severity score >7. Elevated plasma homocysteine (HHcy) was significantly associated with disease severity among HbSS subjects (OR=17.2, CI: 3.490-86.079; p=0.0001). Conversely, no significant association was observed with the mutant genotypes MTR 2756 AG/GG and disease severity (p>0.05). CONCLUSION: While HHcy is significantly associated with phenotypic expression of HbSS, the MTR 2756 SNPs did not appear to independently influence homocysteine level or disease severity in HbSS subjects.

CONTEXTE: La drépanocytose est la maladie génétique la plus répandue au Nigeria, affectant 2 à 3 % d'une population estimée à 160 millions de personnes. Le rôle des mutations génétiques dans les gènes du cycle du folate, et les expressions phénotypiques variables constituant la gravité de la maladie, doivent être examinés de façon critique. OBJECTIF: Cette étude a été menée pour établir le schéma des mutations du gène de la méthionine synthase (rs1805087 SNP), et son association possible avec la gravité de la maladie chez les adultes atteints de drépanocytose à Lagos, au Nigeria. MÉTHODOLOGIE: Il s'agit d'une étude transversale de soixantedix (70) sujets atteints de drépanocytose (HbSS) appariés pour l'âge et le sexe avec des sujets connus apparemment sains de génotype d'hémoglobine AA (HbAA), comme cas et contrôles respectivement. Des questionnaires structurés ont été utilisés pour obtenir des données démographiques, cliniques et autres données phénotypiques nécessaires au calcul de la gravité de la maladie. Le profil de la mutation du gène MTR A2756G et le dosage de l'homocystéine (Hcy) ont été évalués respectivement par réaction en chaîne par polymérase et par test immunologique enzymatique. L'analyse de la formule sanguine complète des participants a été effectuée à l'aide de l'analyseur automatisé KX-21 (Sysmex Corporation, Japon). RÉSULTATS: Les génotypes mutants MTR 2756 AG/GG ont été enregistrés chez 46,4 % (n =55) des sujets présentant un score de gravité de la maladie > 7. L'homocystéine plasmatique élevée (HHcy) était significativement associée à la gravité de la maladie chez les sujets HbSS (OR=17,2, CI : 3,490­86,079 ; p=0,0001). À l'inverse, aucune association significative n'a été observée entre les génotypes mutants MTR 2756 AG/GG et la gravité de la maladie (p>0,05). CONCLUSION: Alors que l'HHcy est significativement associée à l'expression phénotypique de l'HbSS, les SNP MTR 2756 ne semblent pas influencer indépendamment le niveau d'homocystéine ou la gravité de la maladie chez les sujets HbSS.

Sequence analysis for SNP detection and phylogenetic reconstruction of SARS-cov-2 isolated from Nigerian COVID-19 cases.

BACKGROUND: Coronaviruses are a group of viruses that belong to the Family Coronaviridae, genus Betacoronavirus. In December 2019, a new coronavirus disease (COVID-19) characterized by severe respiratory symptoms was discovered. The causative pathogen was a novel coronavirus known as 2019-nCoV and later as SARS-CoV-2. Within two months of its discovery, COVID-19 became a pandemic causing widespread morbidity and mortality. METHODOLOGY: Whole genome sequence data of SARS-CoV-2 isolated from Nigerian COVID-19 cases were retrieved by downloading from GISAID database. A total of 18 sequences that satisfied quality assurance (length ≥29,700 nts and number of unknown bases denoted as "N" ≤ 5%) were used for the study. In addition, genome sequence of SARS-CoV-2 obtained from Nigeria's COVID-19 index case (Accession ID: EPI_ISL_413550) and the reference genome (Accession NC_ 045512.2) were obtained from GISAID and the GenBank databases, respectively. Multiple sequence alignment (MSA) was done in MAFFT (Version 7.471) while SNP calling was implemented in DnaSP (Version 6.12.03), respectively and then visualized in Jalview (Version 2.11.1.0). Phylogenetic analysis was with MEGA X software. RESULTS: Nigerian SARS-CoV-2 had 99.9% genomic similarity with four large conserved genomic regions. A total of 66 SNPs were identified out of which 31 were informative. Nucleotide diversity assessment gave Pi = 0.00048 and average SNP frequency of 2.22 SNPs per 1000 nts. Non-coding genomic regions particularly 5'UTR and 3'UTR had a SNP density of 3.77 and 35.4, respectively. The region with the highest SNP density was ORF10 with a frequency of 8.55 SNPs/1000 nts). This value was significantly higher (P < 0.01) than that of the spike gene, the region of greatest interest in SARS-CoV-2 genomics. Majority (72.2%) of viruses in Nigeria are of L lineage with preponderance of D614G mutation which accounted for 11 (61.1%) out of the 18 viral sequences. Nigeria SARS-CoV-2 revealed 3 major clades namely Oyo, Ekiti and Osun on a maximum likelihood phylogenetic tree. CONCLUSION AND RECOMMENDATION: There was a preponderance of L lineage (to include the new lineage scheme) and D614G mutants. Nigerian SARS-CoV-2 genome revealed ORF1ab as the region containing the highest SNP density as compared to the spike gene. The implication of this distribution of SNPs for the empirical lower infectivity of SARS-CoV-2 in Nigeria is discussed. This also underscores the need for more aggressive testing and treatment of COVID-19 in Nigeria. Additionally, attempt to produce testing kits for COVID-19 in Nigeria should consider the conserved regions identified in this study. Strict adherence to COVID-19 preventive measure is recommended in view of Nigerian SARS-CoV-2 phylogenetic clustering pattern, which suggests intensive community transmission possibly rooted in communal culture characteristic of many ethnicities in Nigeria.

Assessment of MTR Rs1805087 SNP as Possible Modifier ofSickle Cell Disease Severity in a Nigerian Population

BACKGROUND: Sickle cell disease is the commonest geneticdisorder in Nigeria, affecting 2­3% of an estimated population of 160million people. The role of genetic mutations in folate cycle genes,and the variable phenotypic expressions constituting disease severity,needs to be critically examined.OBJECTIVE: This study was carried out to establish the pattern ofmethionine synthase gene mutations (rs1805087 SNP), and its possibleassociation with disease severity in adults with sickle cell anaemia inLagos, Nigeria.METHODOLOGY: This is a cross-sectional study of seventy (70)subjects with sickle cell disease (HbSS) matched for age and genderwith known apparently healthy haemoglobin genotype AA (HbAA)subjects, as cases and controls respectively. Structured questionnaireswere used to obtain demographic, clinical and other phenotypic dataneeded to compute disease severity. Pattern of MTR A2756G genemutation and homocysteine assay (Hcy) were assessed by PolymeraseCh ain Reaction and Enzyme- linked Immun osorbent Assayrespectively. Full blood count analysis of participants was done usingthe KX-21 Automated Analyzer (Sysmex Corporation, Japan).RESULTS: The mutant genotypes MTR 2756 AG/GG were recordedin 46.4% (n =55) of subjects with disease severity score >7. Elevatedplasma homocysteine (HHcy) was significantly associated withdisease severity among HbSS subjects (OR=17.2, CI: 3.490-86.079;p=0.0001). Conversely, no significant association was observed withthe mutant genotypes MTR 2756 AG/GG and disease severity(p>0.05).CONCLUSION: While HHcy is significantly associated withphenotypic expression of HbSS, the MTR 2756 SNPs did not appearto independently influence homocysteine level or disease severity inHbSS subjects

Epigenetic Modification in Methylene Tetrahydrofolate Reductase (MTHFR) Gene of Women with Pre-eclampsia.

BACKGROUND: Genetic and epigenetic factors play significant roles in the aetio-pathogenesis of pre-eclampsia (PE). The effects may vary across racial and geographical boundaries. The role of epigenetic modification in pre-eclampsia was studied among African populations in Lagos, Nigeria. AIM AND OBJECTIVES: This study aimed to determine the pattern of Methylene tetrahydrofolate reductase gene (MTHFR) CpG island methylation in pre-eclampsia, and evaluate associated covariates. METHODOLOGY: This study was an observational, cross-sectional, study conducted at the Lagos University Teaching Hospital and the Lagos State Island Maternity Hospital. A total of 400 pregnant women consisting of 200 pregnant women diagnosed with pre-eclampsia (study group) and 200 pregnant normotensive and apparently healthy women (control group) were recruited for the study. Demographic and clinical histories were obtained through questionnaires. The DNA Methylation status of the CpG Island in promoter region of the MTHFR gene was assessed using bisulphite conversion and methylation specific PCR method. The biochemical parameters measured in the study were: red cell folate, vitamin B12, plasma homocysteine (Hcy) and methylene tetrahydrofolate reductase enzyme level. RESULTS: Homozygous MTHFR CpG island hypomethylation pattern was significantly associated with pre-eclampsia (χ 2 = 22.96; p = 0.000), Mean values of plasma homocysteine in PE women with homozygous hypomethylation (26.1 ± 9.1 umol/L) were significantly higher than (20.1 ± 4.2 umol/L) observed in PE subjects with homozygous hypermethylation (p = 0.008). Homozygous CpG island hypomethylated pattern of the MTHFR promoter region, was associated with the lowest median MTHFR enzyme level (72.8 ± 39.8 pmol/L) compared with heterozygous methylated pattern (91.3 ± 60.9 pmol/L; p = 0.047) and homozygous methylated pattern (82.3 ± 31.0 pmol/L; 0.047). Red cell folate and Vitamin B12 levels were not significantly associated with CpG island methylation status. CONCLUSION: Epigenetic modification plays significant role in the pathogenesis of pre-eclampsia.

Methylene tetrahydrofolate reductase and methionine synthase gene polymorphisms as genetic determinants of pre-eclampsia.

BACKGROUND: Pre-eclampsia (PE) is a leading cause of maternal and neonatal mortality in Africa; and has been associated with the interplay of genetic, metabolic and environmental factors. Polymorphisms of methylene tetrahydrofolate reductase (MTHFR) and methionine synthase (MTR) folate cycle genes, have been controversially associated with pre-eclampsia in studies from different human populations. OBJECTIVES: To determine the distribution of MTHFR C677T and MTR A2756G polymorphisms in a Nigerian population and evaluate possible associations with the occurrence of pre-eclampsia and homocysteine metabolic derangement. MATERIALS AND METHODS: This study was a hospital based study carried out in Lagos, South-western Nigeria. Two hundred pregnant women clinically diagnosed with pre-eclampsia (study group) and 200 apparently healthy non-pre-eclamptic pregnant women (control group) were recruited for the study after written informed consent. Pre-eclampsia was diagnosed based on the International Society for the Study of Hypertension in Pregnancy re-classification of 2013. MTHFR C677T and MTR A2756G polymorphisms were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Statistical analyzes were performed using SPSS version 23. Hardy-Weinberg distribution were tested with χ2 test. Logistic regression model was used to evaluate the relationship of variables with pre-eclampsia. A value of p < 0.05 was considered statistically significant. RESULTS: MTHFR genotype frequencies of CC, CT and TT were 59.8%; 31.2% and 9.0% in study group and 76.6%; 22.3% and 1.0% in the control group respectively. MTR A2756G genotype frequencies of AA, AG and GG genotypes were 71.9%; 20.1% and 8.0% for the study group and 81.5%; 16.4% and 2.1% for the control group. Occurrence of pre-eclampsia was significantly associated with presence of T allele of MTHFR (OR = 1.855; p < 0.05) and G allele of MTR genes (OR = 1.269; p < 0.05), Homozygosity of TG haplotype significantly increased the occurrence of pre-eclampsia among Nigerian women (OR = 2.252; p < 0.05). Population attributable risk fraction percent for the T and G alleles were 16.4% and 11.5% respectively. Mean plasma Hcy level was not, however, significantly affected by MTHFR/MTR haplotypes (F = 1.54; p = 0.157). CONCLUSION: MTHFR C677T and MTR A2756G polymorphisms were associated with pre-eclampsia in a population of pregnant women in Lagos, Nigeria.

Methylenetetrahydrofolate Reductase Enzyme Level and Antioxidant Activity in Women with Gestational Hypertension and Pre-eclampsia in Lagos, Nigeria.

BACKGROUND: Deficiencies of enzymes in the folate cycle may lead to the generation of homocysteine, a toxic metabolic intermediate with pro-oxidant effect and ability to induce oxidant stress and lipid peroxidation as part of the pathophysiological process in gestational hypertension (GH) and pre-eclampsia (PE). AIM: The aim of this study is to assess the reliability of plasma homocysteine (hcy) 5, 10 methylenetetrahydrofolate reductase (MTHFR) enzyme and oxidative stress parameters as indicators of aetio-pathogenesis and severity of gestational hypertension and pre-eclampsia. SUBJECTS AND METHODS: This was a comparative cross-sectional study conducted over 6 months. Two hundred pregnant women were recruited from two sites. They were divided into gestation hypertension (n = 40), pre-eclampsia (n = 60) and control groups (n = 100). Parameters evaluated for statistical analysis were MTHFR enzyme level, plasma homocysteine and malondialdehyde (MDA) levels, with glutathione (GSH), superoxide dismutase (SOD) and catalase (CAT) activities. RESULTS: Mean plasma hcy level and MDA were significantly higher in pre-eclampsia and gestational hypertension when compared to control group (p < 0.05). However, MTHFR enzyme level, GSH, SOD and CAT were significantly higher in normotensive females when compared to PE and GH subgroups (p < 0.05). Pre-eclampsia was significantly associated with an increased risk of lipid peroxidation (OR = 4.923; p = 0.007). CONCLUSION: Pre-eclampsia and gestational hypertension are associated with marked homocysteine metabolic derangement and increased lipid peroxidation induced by oxidative stress and reduced MTHFR enzyme activity which may be the significant risk factors in the aetio-pathogenesis of GH and PE.

Morphological and genetic variation in Tilapia guineensis in West African coastal waters: A mini review.

Tilapia guineensis, a typical estuarine cichlid species in the West Coast of Africa, is an important fish species in view of its immense contribution to the need of many African nations in terms of nutrition, growth and development. Knowledge of how genetically diverse and the genetic structure of T. guineensis especially with regard to the variation in the genetic constitution of T. guineensis populations in this region will be crucial for improving the fish through rational-breeding, proper management, aquaculture production, and stock conservation. Keeping in view the significance of genetic diversity in fish species, report of studies on T. guineensis genetic diversity in West Africa was reviewed. Morphological and molecular techniques were used to assess genetic diversity of this species for breeding and conservation purposes. We hereby report the extent and pattern of variation in genetic constitution of T. guineensis populations found in some West African countries including Nigeria.

Detection of BCR-ABL1 fusion gene transcripts in the saliva of Nigerian patients with chronic myeloid leukemia.

BACKGROUND: The presence of BCR-ABL1 fusion gene resulting from a t(9; 22) reciprocal chromosome translocation is the molecular hallmark of chronic myeloid leukemia (CML). In the diagnosis and treatment of CML, peripheral blood or bone marrow samples are usually taken for analysis. However, both methods are invasive sample collection methods, thus a noninvasive saliva sample method for the detection of the fusion gene transcripts (BCR-ABL) was investigated in some Nigerians with CML. MATERIALS AND METHODS: Real-time (RT)-polymerase chain reaction (PCR) analysis was used to detect BCR-ABL1 fusion gene in the saliva and blood of 42 Nigerian CML patients. RNA was extracted using RNeasy kit and reverse transcribed by random hexamer priming using murine Moloney reverse transcriptase. BCR-ABL1 transcript types were first detected by multiplex PCR and then quantified by a duplex RT-PCR-TaqMan chemistry with MGB probe and Black Hole Quencher. RESULTS: Of the 42 subjects, transcript types were detected in 36 (85.7%) samples, e13a2 fusion transcript sub-type was detected in 9 (21.4%), whereas e14a2 subtype was found in 27 (67.3%); six (14.3%) of the samples did not reveal any of the fusion transcript subtypes. The median BCR-ABL1 messenger RNA values were 9.38 × 102 in saliva and 10.29 × 104 in blood (P < 0.05). Similarly, the median ABL1 value in saliva (3.11 × 103) was significantly lower (P < 0.01) than in blood (4.22 × 103). However, the median BCR-ABL1 ratio in saliva (14.5%) was not significantly different (P = 0.8) from that of blood (12.0%). CONCLUSION: Saliva may offer an alternative easy-to-collect, readily available, and noninvasive sample for the diagnosis and treatment of CML.

Parental determinants of offspring head circumference using a sample of patients attending a government hospital in Lagos, Nigeria.

BACKGROUND: Head circumference at birth is an important neonatal parameter in view of its association with perinatal and postnatal morbidity and mortality. It is an indicator of brain volume and a tool for assessing the development of the central nervous system. Being a complex hereditary trait, predicting baby's head circumference from parental anthropometrics could complement the already existing ultrasonographic method of prediction. OBJECTIVE: To identify the parental anthropometric determinants of baby's head circumference in Lagos, Nigeria, using a sample of patients attending a government hospital. METHODS: Parental anthropometric parameters were obtained from 250 couples. The baby's head circumference was measured immediately after birth. The data were subjected to multivariate analysis. RESULTS: The parental variables that were most predictive of babies' head circumference were mid-parental weight, maternal height, maternal weight gain during pregnancy and maternal age. CONCLUSION: Assessment of these parental attributes can complement ultrasonographic data in predicting baby's head circumference for better perinatal outcome.

Evaluation of association between digital dermatoglyphic traits and type-2 diabetes in Lagos, Nigeria.

BACKGROUND: Diabetes is a very serious problem in the world today. In particular, the incidence of type-2 diabetes is rising in developing countries because of life style changes to that of westernized societies. Type-2 diabetes is usually a late onset disease. Thus, early identification of risk group individuals through a non-invasive method like dermatoglyphics will be very helpful. OBJECTIVE: To see whether finger print pattern (dermatoglyphics) is associated with type-2 diabetes. METHODS: Dermatoglyphic data were obtained from nondiabetic and type-2 diabetic subjects attending the Diabetic Clinic of Lagos University Teaching Hospital (LUTH) using a computer-assisted data capture system. The data were then analysed for association between the dermatoglyphic pattern and the subjects' health status with respect to type-2 diabetes. RESULTS: Total finger ridge count (TFRC) was significantly higher (P < 0.05) in diabetic subjects than in non-diabetics. Results of cluster analysis suggested that dermatoglyphic pattern is associated with type-2 diabetes. CONCLUSION: In view of the association between finger print pattern and type-2 diabetes, dermatoglyphics may be used for early identification of risk group individuals for surveillance purposes with a view to preventing disease onset.