Papers by Rodrigo Moura-neto
PLOS ONE, Apr 22, 2022
The melanocortin-1 receptor (MC1R) is one of the key proteins involved in the regulation of melan... more The melanocortin-1 receptor (MC1R) is one of the key proteins involved in the regulation of melanin production and several polymorphisms have been associated with different phenotypes of skin and hair color in human and nonhuman species. Most of the knowledge is centered on more homogeneous populations and studies involving an admixed group of people should be encouraged due to the great importance of understanding the human color variation. This work evaluates the MC1R diversity and the possible impacts of MC1R variants in an admixed sample population of Rio de Janeiro, Brazil, which is a product of Native American, African, and European miscegenation. Sequencing of complete coding region and part of the 3´UTR of MC1R gene identified 31 variants including one insertion and three novel synonymous substitutions in sample population grouped according to skin, hair and eye pigmentation levels. In nonmetric multidimensional scaling analysis (NMDS), three main clusters were identified, in which the Brazilian dark skin group remained in the African cluster whereas the intermediate and the light skin color phenotype in the European one. None gathered with Asians since their immigration to Brazil was a recent event. In silico analyses demonstrated that Cys35Tyr, Ile155Thr and Pro256Ser, found in our population, have a negative effect on receptor function probably due to changes on the receptor structure. Notably, Cys35Tyr mutation could potentially impair agonist binding. Altogether, this work contributes to the understanding of the genetic background of color variation on an admixed population and gives insights into the damaging effects of MC1R variants.
Forensic Science International-genetics, May 1, 2021
Since 2013, STRait Razor has enabled analysis of massively parallel sequencing (MPS) data from va... more Since 2013, STRait Razor has enabled analysis of massively parallel sequencing (MPS) data from various marker systems such as short tandem repeats, single nucleotide polymorphisms, insertion/deletions, and mitochondrial DNA. In this paper, STRait Razor Online (SRO), available at https://www.unthsc.edu/straitrazor, is introduced as an interactive, Shiny-based user interface for primary analysis of MPS data and secondary analysis of STRait Razor haplotype pileups. This software can be accessed from any common browser via desktop, tablet, or smartphone device. SRO is available also as a standalone application and open-source R script available at https://github.com/ExpectationsManaged/STRaitRazorOnline. The local application is capable of batch processing of both fastq files and primary analysis output. Processed batches generate individual report folders and summary reports at the locus- and haplotype-level in a matter of minutes. For example, the processing of data from ∼700 samples generated with the ForenSeq Signature Preparation Kit from allsequences.txt to a final table can be performed in ∼40 min whereas the Excel-based workbooks can take 35-60 h to compile a subset of the tables generated by SRO. To facilitate analysis of single-source, reference samples, a preliminary triaging system was implemented that calls potential alleles and flags loci suspected of severe heterozygote imbalance. When compared to published, manually curated data sets, 98.72 % of software-assigned allele calls without manual interpretation were consistent with curated data sets, 0.99 % loci were presented to the user for interpretation due to heterozygote imbalance, and the remaining 0.29 % of loci were inconsistent due to the analytical thresholds used across the studies.
Journal of Forensic Sciences, Sep 1, 1997
Fixed bin frequencies for the VNTR loci D1S7, D2S44, D4S139, D5S110, D10S28, and D14S13 were dete... more Fixed bin frequencies for the VNTR loci D1S7, D2S44, D4S139, D5S110, D10S28, and D14S13 were determined in a Rio de Janeiro sample population. The data were generated by RFLP analysis of HaeIII-digested genomic DNA and chemiluminescent detection. The six VNTR loci meet Hardy-Weinberg expectations, and there is no evidence for association of alleles between the VNTR loci. The frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a DNA profile in the general Brazilian population.
Viruses
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the COVID-19 ... more The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the COVID-19 outbreak, posed a primary concern of public health worldwide. The most common changes in SARS-CoV-2 are single nucleotide substitutions, also reported insertions and deletions. This work investigates the presence of SARS-CoV-2 ORF7a deletions identified in COVID-19-positive individuals. Sequencing of SARS-CoV-2 complete genomes showed three different ORF7a size deletions (190-nt, 339-nt and 365-nt). Deletions were confirmed through Sanger sequencing. The ORF7a∆190 was detected in a group of five relatives with mild symptoms of COVID-19, and the ORF7a∆339 and ORF7a∆365 in a couple of co-workers. These deletions did not affect subgenomic RNAs (sgRNA) production downstream of ORF7a. Still, fragments associated with sgRNA of genes upstream of ORF7a showed a decrease in size when corresponding to samples with deletions. In silico analysis suggests that the deletions impair protein proper func...
International Journal of Infectious Diseases, 2021
Hepatitis C virus (HCV) is a global public health problem. Second-generation direct-acting antivi... more Hepatitis C virus (HCV) is a global public health problem. Second-generation direct-acting antivirals targeting non-structural regions on the viral genome are the cornerstone for treatment of chronic infection. However, resistance-associated variants (RAVs) have been reported to be associated with therapeutic failure. The aim of this study was to assess the frequency of variants, including RAVs, in the NS3, NS5A and NS5B regions at baseline in Brazilian patients with chronic hepatitis C with HCV genotypes 1a, 1b and 3a. Serum samples from 13 patients were used to obtain viral RNA. Massively parallel sequencing was performed using genotype-specific amplicons and a panel of Ampliseq technology for all genotypes. Several non-synonymous substitutions were detected at baseline for 11 responders and pre-/post-treatment for two non-responders. HCV genotype 3a was found to have significantly more non-synonymous substitutions than HCV genotype 1 in the NS3 and NS5A regions. Analyses were conducted using quantitative and qualitative inter- and intrapatient comparisons. Variants that confer resistance to the treatment used by the patients were found in both responders and non-responders. A wide frequency distribution of RAVs was found at baseline, and this did not interfere with the achievement of a sustained response. Evaluation of the presence of RAVs requires additional study in order to determine clinical relevance.
Forensic Science International: Genetics, 2021
Forensic DNA typing typically relies on the length-based (LB) separation of PCR products containi... more Forensic DNA typing typically relies on the length-based (LB) separation of PCR products containing short tandem repeat loci (STRs). Massively parallel sequencing (MPS) elucidates an additional level of STR motif and flanking region variation. Also, MPS enables simultaneous analysis of different marker-types - autosomal STRs, SNPs for lineage and identification purposes, reducing both the amount of sample used and the turn-around-time of analysis. Therefore, MPS methodologies are being considered as an additional tool in forensic genetic casework. The PowerSeq™ Auto/Y System (Promega Corp), a multiplex forensic kit for MPS, enables analysis of the 22 autosomal STR markers (plus Amelogenin) from the PowerPlex® Fusion 6C kit and 23 Y-STR markers from the PowerPlex® Y23 kit. Population data were generated from 140 individuals from an admixed sample from Rio de Janeiro, Brazil. All samples were processed according to the manufacturers' recommended protocols. Raw data (FastQ) were generated for each indexed sample and analyzed using STRait Razor v2s and PowerSeqv2.config file. The subsequent population data showed the largest increase in expected heterozygosity (23%), from LB to sequence-based (SB) analyses at the D5S818 locus. Unreported allele was found at the D21S11 locus. The random match probability across all loci decreased from 5.9 × 10-28 to 7.6 × 10-33. Sensitivity studies using 1, 0.25, 0.062 and 0.016 ng of DNA input were analyzed in triplicate. Full Y-STR profiles were detected in all samples, and no autosomal allele drop-out was observed with 62 pg of input DNA. For mixture studies, 1 ng of genomic DNA from a male and female sample at 1:1, 1:4, 1:9, 1:19 and 1:49 proportions were analyzed in triplicate. Clearly resolvable alleles (i.e., no stacking or shared alleles) were obtained at a 1:19 male to female contributor ratio. The minus one stutter (-1) increased with the longest uninterrupted stretch (LUS) allele size reads and according to simple or compound/complex repeats. The haplotype-specific stutter rates add more information for mixed samples interpretation. These data support the use of the PowerSeqTM Auto/Y systems prototype kit (22 autosomal STR loci, 23 Y-STR loci and Amelogenin) for forensic genetics applications.
International Journal of Microbiology, 2020
Molecular detection and classification of the bacterial groups in a sample are relevant in severa... more Molecular detection and classification of the bacterial groups in a sample are relevant in several areas, including medical research and forensics. Sanger sequencing of the 16S rRNA gene is considered the gold standard for microbial phylogenetic analysis. However, the development of massively parallel sequencing (MPS) offers enhanced sensitivity and specificity for microbiological analyses. In addition, 16S rRNA target amplification followed by MPS facilitates the combined use of multiple markers/regions, better discrimination of sample background, and higher sample throughput. We designed a novel set of 16S rRNA gene primers for detection of bacterial species associated with clinical, bioweapon, and biohazards microorganisms via alignment of 364 sequences representing 19 bacterial species and strains relevant to medical and forensics applications. In silico results indicated that the hypervariable regions (V1V2), (V4V5), and (V6V7V8) support the resolution of a selected group of ba...
International journal of legal medicine, Jan 2, 2018
Forensic science international. Genetics, Jan 18, 2018
Sequencing whole mitochondrial genomes by capillary electrophoresis is a costly and time/labor-in... more Sequencing whole mitochondrial genomes by capillary electrophoresis is a costly and time/labor-intensive endeavor. Many of the previous Sanger sequencing-based approaches generated amplicons that were several kilobases in length; lengths that are likely not amenable for most forensic applications. However, with the advent of massively parallel sequencing (MPS) short-amplicon multiplexes covering the entire mitochondrial genome can be sequenced relatively easily and rapidly. Recently, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific by Applied Biosystems™) has been introduced. This panel is composed of 162 amplicons (in two multiplexes) that are considerably smaller in length (∼163bp) and thus are more amenable to analyzing challenged samples. This panel was evaluated on both the Ion S5™ System (Thermo Fisher Scientific) and the MiSeq™ FGx Desktop Sequencer (Illumina). A script was developed to extract phased haplotypes associated with these amplicons. Levels of re...
International journal of legal medicine, Jan 26, 2017
CYP2D6 is a critical pharmacogenetic target, and polymorphisms in the gene region are commonly us... more CYP2D6 is a critical pharmacogenetic target, and polymorphisms in the gene region are commonly used to infer enzyme activity score and predict resulting metabolizer phenotype: poor, intermediate, extensive/normal, or ultrarapid which can be useful in determining cause and/or manner of death in some autopsies. Current genotyping approaches are incapable of identifying novel and/or rare variants, so CYP2D6 star allele definitions are limited to polymorphisms known a priori. While useful for most predictions, recent studies using massively parallel sequencing data have identified additional polymorphisms in CYP2D6 that are predicted to alter enzyme function but are not considered in current star allele nomenclature. The 1000 Genomes Project data were used to produce full-gene haplotypes, describe their distribution in super-populations, and predict enzyme activity scores. Full-gene haplotypes generated lower activity scores than current approaches due to inclusion of additional damagin...
International Journal of Legal Medicine, 2017
The use of bi-allelic markers such as retrotransposable element insertion polymorphisms or Innuls... more The use of bi-allelic markers such as retrotransposable element insertion polymorphisms or Innuls (for insertion/null) can overcome some limitations of short tandem repeat (STR) loci in typing forensic biological evidence. This study investigated the efficiency of the InnoTyper® 21 Innul markers in an urban admixed population sample in Rio de Janeiro (n = 40) and one highly compromised sample collected as evidence by the Rio de Janeiro police. No significant departures from Hardy-Weinberg equilibrium were detected after the Bonferroni correction (α′ ≈ 0.05/20, p < 0.0025), and no significant linkage disequilibrium was observed between markers. Assuming loci independence, the cumulative random match probability (RMP) was 2.3 × 10 −8. A lower mean Fis value was obtained for this sample population compared with those of three North American populations (African-American, Southwest Hispanic, US Caucasian). Principal component analysis with the three North American populations and one from 21 East Asian population showed that African Americans segregated as an independent group while US Caucasian, Southwest Hispanic, East Asian, and Rio de Janeiro populations are in a single large heterogeneous group. Also, a full Innuls profile was produced from an evidence sample, despite the DNA being highly degraded. In conclusion, this system is a useful complement to standard STR kits.
Forensic science international. Genetics, Jul 19, 2016
Geographically, the UAE is situated along the coast of the southern Arabian Gulf Sea, sharing bor... more Geographically, the UAE is situated along the coast of the southern Arabian Gulf Sea, sharing borders with Oman and Saudi Arabia. The indigenous inhabitants are called Emirati and constitute only 20% of the total population. The rest of the population is migrants and include South Asians (Indians, Pakistanis and Bangladeshis), Afghanis, Iranians, and people from other Arab countries such as Palestine, Yemen and Oman (www.vesitabudhabi.ae). This study assessed Y-STR population variation in the UAE that could provide relevant forensic information for the Emirates as well as other countries around the world. Whole blood samples from 278 unrelated, male individuals from UAE populations were collected with informed consent and placed on FTA 1 cards (Whatman, UK) following the lab's standard operating protocol. Disks (1.2-mm diameter) were punched out of a bloodstained FTA-card and placed directly into a Microtiter plate (Eppendorf, Hamburg, Germany) using a BSD600-duet puncher (BSD Robotics, Brendale, QLD, Australia). Amplification was carried out on a GeneAmp 1 PCR System 9700 thermal cycler (Life Technologies, South San Francisco, CA) using the reagents in the PowerPlex 1 Y23 System (Promega Corporation, Madison, WI) and following the manufacturer's recommended protocol. The PCR products were prepared and run on Applied Biosystems 3500xL Genetic Analyzer using POP-41 polymer and a 36-cm 3500xL 24-capillary array according to the manufacturer's recommended protocol. Data were analyzed with GeneMapper 1 ID-X Software v1.4 software (Life Technologies). Population based analyses were performed using the open source R statistical computing program (http://www.r-project.org/) and standard built-in functions. Genotypes of twenty-one Ychromosome markers from five populations were included in the study. The DYS385a/b locus was not considered, and the number of repeats in DYS389I was subtracted from those of DYS389II, so that its diversity was not considered twice. Chromosomes with duplicated alleles at a locus were removed from the analyses. Four populations belong to the Middle East and they are UAE, Kuwait, Iraq, and Lebanon. An East Asian population from the Philippines was used as an out-group (Table 1). The populations were combined to form a population denoted as "All". This population was created to give an overview of the markers' summary statistics and to provide a reference by which any population can be compared.
International journal of legal medicine, Jan 8, 2015
Ancestry informative markers (AIMs) can be used to detect and adjust for population stratificatio... more Ancestry informative markers (AIMs) can be used to detect and adjust for population stratification and predict the ancestry of the source of an evidence sample. Autosomal single nucleotide polymorphisms (SNPs) are the best candidates for AIMs. It is essential to identify the most informative AIM SNPs across relevant populations. Several informativeness measures for ancestry estimation have been used for AIMs selection: absolute allele frequency differences (δ), F statistics (F ST), and informativeness for assignment measure (In). However, their efficacy has not been compared objectively, particularly for determining affiliations of major US populations. In this study, these three measures were directly compared for AIMs selection among four major US populations, i.e., African American, Caucasian, East Asian, and Hispanic American. The results showed that the F ST panel performed slightly better for population resolution based on principal component analysis (PCA) clustering than did...
International journal of legal medicine, 2015
The majority of STR loci are not ideal for the analysis of forensic samples with degraded and/or ... more The majority of STR loci are not ideal for the analysis of forensic samples with degraded and/or low template DNA. One alternative to overcome these limitations is the use of bi-allelic markers, which have low mutation rates and shorter amplicons. Human identification (HID) InDel marker panels have been described in several countries, including Brazil. The commercial kit available is, however, mostly suitable for Europeans, with lower discrimination power for other population groups. Recently, a combination of 49 InDel markers used in four different ethnic groups in the USA has been shown to be more informative than another panel from Portugal, already tested in a Rio de Janeiro sample. However, these 49 InDels have yet to be applied to other admixed or isolated populations. We assessed the efficiency of this panel in two urban admixed populations (Rio de Janeiro, Brazil; Tripoli, Libya) and one isolated Native Brazilian community. All markers are in Hardy-Weinberg equilibrium (HWE)...
Genetics and Molecular Research, 2021
©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 20 (1): gmr18737 C. Bottino et al.... more ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 20 (1): gmr18737 C. Bottino et al. 2 data and contamination control. The second generates haplotypes, allowing haplogroup classification, and biogeographic inference, as well as verification of a matrilineal relationship. This straightforward freeware pipeline for mtDNA data analysis should facilitate the implementation of this type of system in forensic lab routine. Using our pipeline, the definition of the samples being of African origin was more precise when considering the whole mtGenome and not only the control region, which is usually used for routine forensic analysis. The final analysis was consistent with the existence of a matrilineal relationship between the alleged son (bone sample recovered from the sea) and the mother.
Saúde, Ética & Justiça, 2013
RESUMO: Cannabis sativa é uma das espécies mais antigas de plantas domesticadas e permanece como ... more RESUMO: Cannabis sativa é uma das espécies mais antigas de plantas domesticadas e permanece como uma das culturas mais amplamente difundida e a droga ilícita mais consumida no mundo. Há uma grande difi culdade em identifi car e individualizar as amostras de Cannabis sp, difi cultando a correlação a prováveis locais de plantações ilegais, o que permitiria revelar rotas de tráfi co, relacionar grupos criminosos e distinguir amostras legais daquelas comercializadas como droga, onde o cultivo é permitido. A principal fi nalidade do DNA Barcode é o de proporcionar uma rápida e precisa identifi cação de organismos a partir de uma pequena região padronizada do genoma que ajuda a caracterizar e distinguir espécies e indivíduos não identifi cados para atribuir à espécie. Um dos genes candidatos é o ribulose-1,5-bisfosfato carboxilase/oxigenase (rbcL), utilizado como um sistema de DNA Barcode e presente no DNA dos cloroplastos das plantas, sendo o responsável pela produção subunidade maior da que converte dióxido de carbono e água em carboidratos. Nosso objetivo é o desenvolvimento de um protocolo efi ciente de extração de DNA e de sequenciamento do gene rbcL para análise forense de amostras apreendidas da Polícia Judiciária. DNA de amostras de Cannabis sativa,caracterizadas no ICCE/DGPTC/PCERJ, foi extraído utilizandoo Mini DNeasy Plant (Qiagen)no IPPGF/ DGPTC/PCERJ. O material foi transferido para o LabFor/UFRJe um fragmento de 735 pb do gene rbcL foi amplifi cado através de um par de iniciadores descritos na literatura como universais para plantas.O fragmento foi sequenciado, com o protocolo do BigDye v3.1, usando ABI 3500 (Life Technologies). As comparações das sequências foram realizadas no software Geneious (Biomatters). A nossa sequência consenso de 559 pb foi comparada às seqüências que correspondem às regiões rbcL em Cannabis sativa depositadas no GenBank, e observamos a ocorrência de polimorfi smos (SNPs) entre as amostras dos Estados unidos, Reino Unido e China, sugerindo que se trata de uma assinatura genética para análise forense.
Forensic Science International: Genetics, 2019
Highlights The Precision ID mtDNA Whole Genome Panel was evaluated in a large lineage study usi... more Highlights The Precision ID mtDNA Whole Genome Panel was evaluated in a large lineage study using different tissues Samples included high quality reference samples and also challenging forensic samples The vast majority of samples yielded full mitogenomes from diverse phylogenetic backgrounds We observed very high concordance to previous Sanger and other MPS-based analyses We observed differences in the display of heteroplasmy that deserve further research
International Journal of Legal Medicine, 2011
Population data of 15 short tandem repeat loci of the AmpFlSTR® next generation multiplex (NGM)™ ... more Population data of 15 short tandem repeat loci of the AmpFlSTR® next generation multiplex (NGM)™ were obtained from a sample of 835 individuals. The loci are the ten short tandem repeats (STRs) in the SGM Plus® Kit plus the EDNAP- and ENSFI-recommended STRs D10S1248, D22S1045, D2S441, D1S1656, and D12S391. Allele frequency and other forensically relevant statistics data were generated for the NGM loci into five current country macroregions of Brazil (North, Northeast, Central West, Southeast, and South). All the analyzed loci meet Hardy-Weinberg equilibrium expectations and no linkage disequilibrium in all pairs of loci. The observed and expected heterozygosity, power of discrimination, polymorphic information content, and the other population-genetic indices were calculated. The overall power of discrimination was greater than 0.99999999999999999996 and the combined power of exclusion was greater than 0.9999998 in all Brazilian populations. Comparative analysis between populations from different Brazilian macroregions as well as between Brazil and Caucasian, African Americans, and Hispanic US populations are presented.
Brazilian Journal of Medical and Biological Research, 2008
Our aim was to determine the frequencies of the angiotensin-converting enzyme (ACE) gene alleles ... more Our aim was to determine the frequencies of the angiotensin-converting enzyme (ACE) gene alleles D and I and any associations to cardiovascular risk factors in a population sample from Rio de Janeiro, Brazil. Eighty-four adults were selected consecutively during a 6-month period from a cohort subgroup of a previous large cross-sectional survey in Rio de Janeiro. Anthropometric data and blood pressure measurements, echocardiogram, albuminuria, glycemia, lipid profile, and ACE genotype and serum enzyme activity were determined. The frequency of the ACE*D and I alleles in the population under study, determined by PCR, was 0.59 and 0.41, respectively, and the frequencies of the DD, DI, and II genotypes were 0.33, 0.51, and 0.16, respectively. No association between hypertension and genotype was detected using the Kruskal-Wallis method. Mean plasma ACE activity (U/ mL) in the DD (N = 28), DI (N = 45) and II (N = 13) groups was 43 (in males) and 52 (in females), 37 and 39, and 22 and 27, respectively; mean microalbuminuria (mg/dL) was 1.41 and 1.6, 0.85 and 0.9, and 0.6 and 0.63, respectively; mean HDL cholesterol (mg/dL) was 40 and 43, 37 and 45, and 41 and 49, respectively, and mean glucose (mg/dL) was 93 and 108, 107 and 98, and 85 and 124, respectively. A high level of ACE activity and albuminuria, and a low level of HDL cholesterol and glucose, were found to be associated with the DD genotype. Finally, the II genotype was found to be associated with variables related to glucose intolerance.
International journal of legal medicine, Jan 8, 2015
Ancestry informative markers (AIMs) can be used to detect and adjust for population stratificatio... more Ancestry informative markers (AIMs) can be used to detect and adjust for population stratification and predict the ancestry of the source of an evidence sample. Autosomal single nucleotide polymorphisms (SNPs) are the best candidates for AIMs. It is essential to identify the most informative AIM SNPs across relevant populations. Several informativeness measures for ancestry estimation have been used for AIMs selection: absolute allele frequency differences (δ), F statistics (F ST), and informativeness for assignment measure (In). However, their efficacy has not been compared objectively, particularly for determining affiliations of major US populations. In this study, these three measures were directly compared for AIMs selection among four major US populations, i.e., African American, Caucasian, East Asian, and Hispanic American. The results showed that the F ST panel performed slightly better for population resolution based on principal component analysis (PCA) clustering than did...
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Papers by Rodrigo Moura-neto