1
|
Reis TTAD, Silva JM, Gamba BF, Rodrigues GO, Nascimento PRAD, Topázio BA, Cornélio DA, Nery LFA. FREQUÊNCIA DA PERDA DO CROMOSSOMO Y EM MEDULA ÓSSEA DE PACIENTES COM DOENÇAS HEMATOLÓGICAS. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.1115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
2
|
Barra GB, Santa Rita TH, Mesquita PG, Jácomo RH, Nery LFA. Overcoming Supply Shortage for SARS-CoV-2 Detection by RT-qPCR. Genes (Basel) 2021; 12:90. [PMID: 33450867 PMCID: PMC7828326 DOI: 10.3390/genes12010090] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/22/2020] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
In February 2020, our laboratory started to offer a RT-qPCR assay for the qualitative detection of severe acute respiratory syndrome coronavirus 2. A few months after the assay was released to our patients, some materials, reagents, and equipment became in short supply. Alternative protocols were necessary in order to avoid stopping testing to the population. However, the suitability of these alternatives needs to be validated before their use. Here, we investigated if saliva is a reliable alternative specimen to nasopharyngeal swabs; if 0.45% saline is a reliable alternative to guanidine hydrochloride as a collection viral transport media; the stability of SARS-COV-2 in guanidine hydrochloride and in 0.45% saline for 10 and 50 days at room temperature; and if the primers/probe concentration and thermocycling times could be reduced so as to overcome the short supply of these reagents and equipment, without a significant loss of the assay performance. We found that saliva is not an appropriated specimen for our method-nasopharyngeal swabs perform better. Saline (0.45%) and guanidine hydrochloride have a similar SARS-CoV-2 diagnostic capability as tube additives. Reliable SARS-CoV-2 RNA detection can be performed after sample storage for 10 days at room temperature (18-23 °C) in both 0.45% saline and guanidine hydrochloride. Using synthetic RNA, and decreasing the concentration of primers by five-fold and probes by 2.5-fold, changed the assay limit of detection (LOD) from 7.2 copies/reaction to 23.7 copies/reaction and the subsequent reducing of thermocycling times changed the assay LOD from 23.7 copies/reaction to 44.2 copies/reaction. However, using real clinical samples with Cq values ranging from ~12.15 to ~36.46, the results of the three tested conditions were almost identical. These alterations will not affect the vast majority of diagnostics and increase the daily testing capability in 30% and increase primers and probe stocks in 500% and 250%, respectively. Taken together, the alternative protocols described here overcome the short supply of tubes, reagents and equipment during the SARS-CoV-2 pandemic, avoiding the collapse of test offering for the population: 105,757 samples were processed, and 25,156 SARS-CoV-2 diagnostics were performed from 9 May 2020 to 30 June 2020.
Collapse
|
3
|
Barra GB, Santa Rita TH, Almeida ALSC, Jácomo RH, Nery LFA. Serum Has Higher Proportion of Janus Kinase 2 V617F Mutation Compared to Paired EDTA-Whole Blood Sample: A Model for Somatic Mutation Quantification Using qPCR and the 2 -∆∆Cq Method. Diagnostics (Basel) 2020; 10:E153. [PMID: 32178286 PMCID: PMC7151023 DOI: 10.3390/diagnostics10030153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 12/14/2022] Open
Abstract
Detection of the Janus Kinase-2 (JAK2) V617F mutation is a diagnostic criterion for myeloproliferative neoplasms, and high levels of mutant alleles are associated with worse outcomes. This mutation is usually tested on blood DNA by allele-specific qPCR (AS-qPCR) and measured using absolute quantification. However, some automated DNA extractions co-extracts of PCR inhibitors from blood and qPCR absolute quantification need increased efforts in order to maintain standard curves. JAK2 V617F can also be detected in serum using droplet digital PCR (ddPCR), a specimen with less inhibitors and favorable to automated extractions, but ddPCR instruments are not wide available as qPCR thermocyclers. Here, we evaluate whether JAK2 V617F could be accurately quantified by AS-qPCR using the 2-∆∆Cq method on blood DNA and validate the assay using gold-standard molecular diagnostic protocols. Next, we apply the validated method to assess if the mutation could be reliably detected/quantified in serum. JAK2 V617F could be quantified by AS-qPCR using the 2-∆∆Cq method-the assay was highly accurate (bias of 1.91%) compared to a commercial kit, highly precise (total CV% of 0.40%, 1.92%, 11.12% for samples with 93%, 54%, and 2.5% of mutant allele), highly sensitive (limit of detection of 0.15%), and demonstrated a linear detection response from 1.1% to 99.9%. Serum presented a higher mutant allele burden compared to the paired whole blood (mean of 4%), which allows for an increased JAK2 mutant detection rate and favors increased JAK2 V617F high-throughput analysis.
Collapse
Affiliation(s)
- Gustavo Barcelos Barra
- Sabin Medicina Diagnóstica, SAAN, quadra 3, lote 145/185, Brasilia 70632-300, Brazil; (T.H.S.R.); (A.L.S.C.A.); (R.H.J.); (L.F.A.N.)
- Post-Graduation in Health Science, University of Brasilia, Brasilia 70910-900, Brazil
| | - Ticiane Henriques Santa Rita
- Sabin Medicina Diagnóstica, SAAN, quadra 3, lote 145/185, Brasilia 70632-300, Brazil; (T.H.S.R.); (A.L.S.C.A.); (R.H.J.); (L.F.A.N.)
| | - Ana Luisa Santa Cruz Almeida
- Sabin Medicina Diagnóstica, SAAN, quadra 3, lote 145/185, Brasilia 70632-300, Brazil; (T.H.S.R.); (A.L.S.C.A.); (R.H.J.); (L.F.A.N.)
- Post-Graduation in Health Science, University of Brasilia, Brasilia 70910-900, Brazil
| | - Rafael Henriques Jácomo
- Sabin Medicina Diagnóstica, SAAN, quadra 3, lote 145/185, Brasilia 70632-300, Brazil; (T.H.S.R.); (A.L.S.C.A.); (R.H.J.); (L.F.A.N.)
| | - Lídia Freire Abdalla Nery
- Sabin Medicina Diagnóstica, SAAN, quadra 3, lote 145/185, Brasilia 70632-300, Brazil; (T.H.S.R.); (A.L.S.C.A.); (R.H.J.); (L.F.A.N.)
| |
Collapse
|
4
|
Barra GB, Santa Rita TH, Jardim DP, Mesquita PG, Nobre CS, Jácomo RH, Abdalla Nery LF. Genotyping of Single Nucleotide Polymorphisms Using Allele-Specific qPCR Producing Amplicons of Small Sizes Directly from Crude Serum Isolated from Capillary Blood by a Hand-Powered Paper Centrifuge. Diagnostics (Basel) 2019; 9:diagnostics9010009. [PMID: 30641881 PMCID: PMC6468353 DOI: 10.3390/diagnostics9010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/27/2018] [Accepted: 12/29/2018] [Indexed: 12/26/2022] Open
Abstract
The cell-free genomic DNA (gDNA) concentration in serum ranges from 1500 to 7500 copies/mL within 2 h after phlebotomy (6⁻24 times the concentration observed in plasma). Here, we aimed to evaluate the gDNA size distribution in serum with time after coagulation and to test if crude serum can be directly used as a source of gDNA for qPCR. Next, we investigated if single nucleotide polymorphisms (SNPs) could be genotyped directly from the crude serum isolated from capillary blood using a hand-powered paper centrifuge. All tested PCR targets (65, 100, 202 and 688 base pairs) could be successfully amplified from DNA extracted from serum, irrespective of their amplicon size. The observed qPCR quantitation cycles suggested that the genomic DNA yield increased in serum with incubation at room temperature. Additionally, only 65 and 101 base pair qPCR targets could be amplified from crude serum soon after the coagulation. Incubation for 4 days at room temperature was necessary for the amplification of PCR targets of 202 base pairs. The 688 base pair qPCR target could not be amplified from serum directly. Lastly, serum was successfully separated from capillary blood using the proposed paper centrifuge and the genotypes were assigned by testing the crude serum using allele-specific qPCR, producing small amplicon sizes in complete agreement with the genotypes assigned by testing the DNA extracted from whole blood. The serum can be used directly as the template in qPCR for SNP genotyping, especially if small amplicon sizes are applied. This shortcut in the SNP genotyping process could further molecular point-of-care diagnostics due to elimination of the DNA extraction step.
Collapse
Affiliation(s)
- Gustavo Barcelos Barra
- Sabin Laboratory, Brasília 70632-300, Brazil.
- Post-Graduation of Health Science, University of Brasília, Brasilia 70910-900, Brazil.
| | - Ticiane Henriques Santa Rita
- Sabin Laboratory, Brasília 70632-300, Brazil.
- Post-Graduation of Health Science, University of Brasília, Brasilia 70910-900, Brazil.
| | - Daniella Paniago Jardim
- Sabin Laboratory, Brasília 70632-300, Brazil.
- Post-Graduation of Health Science, University of Brasília, Brasilia 70910-900, Brazil.
| | | | - Camila Santos Nobre
- Sabin Laboratory, Brasília 70632-300, Brazil.
- Post-Graduation of Health Science, University of Brasília, Brasilia 70910-900, Brazil.
| | | | | |
Collapse
|
5
|
Nobre CS, Silva JA, Jácomo RH, Nery LFA, Barra GB. Flow Cytometric Analysis of Erythrocytes Osmotic Fragility in Hereditary Spherocytosis: A Case-Controlled Study Evaluating the Best Anticoagulant, Sample Pre-Treatment and NaCl Concentration for Reliable Screening of this Red Blood Cell Membrane Disorder. Cytometry B Clin Cytom 2018; 94:910-917. [PMID: 30328264 DOI: 10.1002/cyto.b.21733] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 06/22/2018] [Accepted: 07/15/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND The cytometric flow osmotic fragility test (FC-OFT) was recently introduced. However, the test is still under development and some variables have not yet been fully tested. METHODS The osmotic fragility of hereditary spherocytosis (HS) cases and healthy controls were evaluated by FC-OFT using a series of tubes containing decreasing concentrations of NaCl. The analyses were executed in fresh and incubated (37°C for 24 h) blood samples anticoagulated with EDTA and heparin. The percentages of residual red blood cells were used to plot the osmotic fragility curves. The OF curves of each tested condition were compared using the median corpuscular fragility (MCF). ROC curve analyses identified the most accurate NaCl concentrations for differentiation between HS cases and healthy controls. RESULTS FC-OFT curves assumed a sigmoidal dose-response shape and the MCF of cases and controls were different in all instances. MCF comparisons revealed that incubation and anticoagulant have major and minor effects on the FC-OFT, respectively. One hundred percent of sensitivity and specificity was obtained from 5.5 to 6.0 g/L of NaCl in EDTA-treated fresh blood, from 6.0 to 8.0 g/L of NaCl in EDTA-treated incubated blood, and in none of the tested NaCl concentration in heparinized blood. CONCLUSIONS EDTA is the anticoagulant of choice for the assay. Incubation at 37°C for 24 h increased its diagnostic capability. The most reliable NaCl concentration for the discrimination of HS case from controls was 6.0 g/L of NaCL in fresh EDTA-treated blood, and was 7.5 g/L of NaCl in incubated EDTA-treated blood. © 2018 International Clinical Cytometry Society.
Collapse
Affiliation(s)
- Camila Santos Nobre
- Sabin Laboratory, Brasília, Federal District, Brazil.,Post-Graduation of Health Science, University of Brasília, Brasília, Brazil
| | | | | | | | - Gustavo Barcelos Barra
- Sabin Laboratory, Brasília, Federal District, Brazil.,Post-Graduation of Health Science, University of Brasília, Brasília, Brazil
| |
Collapse
|
6
|
Santa Rita TH, Nobre CS, Jácomo RH, Nery LFA, Barra GB. Cover Image, Volume 38, Issue 8. Prenat Diagn 2018. [DOI: 10.1002/pd.5321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
7
|
Santa Rita TH, Nobre CS, Jácomo RH, Nery LFA, Barra GB. Noninvasive fetal sex determination by analysis of cell-free fetal DNA in maternal capillary blood obtained by fingertip puncture. Prenat Diagn 2018; 38:620-623. [PMID: 29655231 DOI: 10.1002/pd.5265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 11/06/2022]
Abstract
What's already known about this topic?
Noninvasive fetal sex determination searches for Y‐chromosome sequences in maternal plasma isolated from venous blood drawn by venipuncture to indicate fetal sex in the first trimester of pregnancy.
Capillary blood collection is much less invasive than venipuncture, thereby offering the possibility of sampling in geographical areas where there is no phlebotomist present.
What does this study add?
Fetal DNA is present in maternal capillary blood allowing for noninvasive fetal sex determination.
Exogenous male DNA may be present, and detectable, on the fingertips of pregnant women.
The elimination of the exogenous male DNA is critical for a reliable fetal sex determination using maternal capillary blood.
A diluted buffered sodium hypochlorite (0.5%‐1%) can be used to eliminate exogenous male DNA from the fingertips of pregnant women.
Collapse
Affiliation(s)
- Ticiane Henriques Santa Rita
- Sabin Laboratory, Brasília, Federal District, Brazil
- Post-Graduation in Health Sciences, University of Brasília, Brasília, Federal District, Brazil
| | - Camila Santos Nobre
- Sabin Laboratory, Brasília, Federal District, Brazil
- Post-Graduation in Health Sciences, University of Brasília, Brasília, Federal District, Brazil
| | | | | | - Gustavo Barcelos Barra
- Sabin Laboratory, Brasília, Federal District, Brazil
- Post-Graduation in Health Sciences, University of Brasília, Brasília, Federal District, Brazil
| |
Collapse
|
8
|
Santa Rita TH, Chianca CF, Nery LFA, Barra GB. Allele frequencies of 38 insertion/deletion polymorphisms in a population sample from the Federal District (Brazil)—A territory that arose from nothing. Forensic Sci Int Genet 2015; 19:79-80. [DOI: 10.1016/j.fsigen.2015.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/12/2015] [Accepted: 06/27/2015] [Indexed: 11/16/2022]
|
9
|
Barra GB, Santa Rita TH, de Almeida Vasques J, Chianca CF, Nery LFA, Santana Soares Costa S. EDTA-mediated inhibition of DNases protects circulating cell-free DNA from ex vivo degradation in blood samples. Clin Biochem 2015; 48:976-81. [PMID: 25746148 DOI: 10.1016/j.clinbiochem.2015.02.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/18/2015] [Accepted: 02/24/2015] [Indexed: 02/07/2023]
Abstract
OBJETIVES The extracellular DNA occurring in plasma-EDTA and serum is a biomarker of growing interest, especially in prenatal diagnosis and oncology. The objectives of the present study were to compare the DNase activity in these specimens and to investigate its ex-vivo impact over the circulating cell-free DNA yield (ccfDNA), using the circulating cell-free fetal DNA (ccffDNA) as a tool. DESIGN AND METHODS EDTA-plasma and serum from women bearing male fetus were submitted to an endogenous DNase activity assay based on qPCR hydrolysis probe degradation, they were treated with DNAse I to investigate the action of an exogenous nuclease and also submitted to different temperature conditions to investigate the temperature-dependent degradation of the ccffDNA. In all instances, all male ccffDNA were quantified by qPCR targeting the Y chromosome-specific sequence DYS-14. Moreover, a serial dilution of EDTA was added to nonanticoagulated plasma and serum before the endogenous DNAse activity assay, to investigate the EDTA-mediated inhibition of the blood's DNase. RESULTS The endogenous nuclease activity was 14.9-fold higher in serum compared to EDTA-plasma. The DNAse I treatment did not alter the ccffDNA yields in EDTA-plasma, but completely degraded it in serum. The addition of increasing doses of EDTA to nonanticoagulated plasma and serum resulted in a stepwise inhibition of their nucleases activity. Finally, we observed a much more pronounced temperature-mediated decrease on the ccffDNA amount in serum compared to EDTA-plasma. CONCLUSION The exogenous and endogenous DNases are more active in serum, the anticoagulant EDTA indirectly inhibits blood DNases, and consequently ccfDNA is protected from the blood's DNase preanalytical impact in EDTA-plasma.
Collapse
Affiliation(s)
- Gustavo Barcelos Barra
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil.
| | - Ticiane Henriques Santa Rita
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil
| | - Júlia de Almeida Vasques
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil
| | | | | | | |
Collapse
|
10
|
Barra GB, Santa Rita TH, Chianca CF, Velasco LFR, de Sousa CF, Nery LFA, Costa SSS. Fetal male lineage determination by analysis of Y-chromosome STR haplotype in maternal plasma. Forensic Sci Int Genet 2014; 15:105-10. [PMID: 25434746 DOI: 10.1016/j.fsigen.2014.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 11/03/2014] [Accepted: 11/06/2014] [Indexed: 01/26/2023]
Abstract
The aim of this study is to determine the fetus Y-STR haplotype in maternal plasma during pregnancy and estimate, non-invasively, if the alleged father and fetus belong to the same male lineage. The study enrolled couples with singleton pregnancies and known paternity. All participants signed informed consent and the local ethics committee approved the study. Peripheral blood was collected in EDTA tubes (mother) and in FTA paper (father). Maternal plasma DNA was extracted by using NucliSens EasyMAG. Fetal gender was determined by qPCR targeting DYS-14 in maternal plasma and it was also confirmed after the delivery. From all included volunteers, the first consecutive 20 mothers bearing male fetuses and 10 mothers bearing female fetuses were selected for the Y-STR analysis. The median gestational age was 12 weeks (range 12-36). All DNA samples were subjected to PCR amplification by PowerPlex Y23, ampFLSTR Yfiler, and two in-house multiplexes, which together accounts for 27 different Y-STR. The PCR products were detected with 3500 Genetic Analyzer and they were analyzed using GeneMapper-IDX. Fetuses' haplotypes (Yfiler format) were compared to other 5328 Brazilian haplotypes available on Y-chromosome haplotypes reference database (YHRD). As a result, between 22 and 27 loci were successfully amplified from maternal plasma in all 20 cases of male fetuses. None of the women bearing female fetuses had a falsely amplified Y-STR haplotype. The haplotype detected in maternal plasma completely matched the alleged father haplotype in 16 out of the 20 cases. Four cases showed single mismatches and they did not configure exclusions; 1 case showed a mutation in the DYS 458 locus due to the loss of one repeat unit and 3 cases showed one DYS 385I/II locus dropout. All mismatches were confirmed after the delivery. Seventeen fetuses' haplotypes were not found in YHRD and one of them had a mutation, which corresponded to the paternity probability of 99.9812% and 95.7028%, respectively. Three fetuses' haplotypes occurred twice in YHRD, which corresponded to paternity probability of 99.9437%. In conclusion, high discriminatory fetal Y-STR haplotype could be determined from maternal plasma during pregnancy starting at 12 weeks of gestation. All male fetuses could be attributed to the alleged father male lineage early in pregnancy. The high probability of paternity associated with each case suggests that the relationship is not random and this strategy can be use as an alternative for male fetal kinship analysis.
Collapse
Affiliation(s)
- Gustavo Barcelos Barra
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil.
| | - Ticiane Henriques Santa Rita
- Sabin Laboratory of Clinical Analysis, Brasilia, Federal District, Brazil; Post-Graduation in Health Sciences, University of Brasilia, Brasilia, Federal District, Brazil
| | | | | | | | | | | |
Collapse
|