Matrix metalloproteinases 7, 8, 12, 13 gene haplotypes associated with colorectal cancer in a Mexican population.

BACKGROUND: Matrix metalloproteinases (MMPs) are involved in tumor invasion and progression in colorectal cancer (CRC). Variants rs11568818, rs11225395, rs2276109 and rs2252070 have been associated with this neoplasm. OBJECTIVE: To evaluate MMPs 7, 8, 12, and 13 haplotypes and their association with CRC. MATERIAL AND METHODS: One-hundred and four patients and 112 healthy individuals were genotyped by polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP). For the association analysis, odds ratio and confidence interval values were calculated. Haplotype and linkage disequilibrium (LD) analysis was performed with Arlequin software, v3.5. RESULTS: LD was present between rs2276109 and rs2252070. Haplotypes rs11568818(A)-rs11225395(T)-rs2276109(A)-rs2252070(A) and rs11568818(A)-rs11225395(C)-rs2276109(A)-rs2252070(G) were associated with CRC risk, and haplotypes rs11568818(G)-rs11225395(C)-rs2276109(A)-rs2252070(A) and rs11568818(A)-rs11225395(T)-rs2276109(A)-rs2252070(G), with protection. CONCLUSION: Variants rs2276109 and rs2252070 showed genetic linkage. Two haplotypes were associated with the development of CRC (ATAA and ACAG) and two were associated with protection (GCAA and ATAG). This study represents the first report on variants rs11225395 and rs2276109 frequency in a Mexican population.

ANTECEDENTES: Las metaloproteinasas (MMP) se involucran en invasión y progresión tumoral en cáncer colorrectal (CCR). Las variantes rs11568818, rs11225395, rs2276109 y rs2252070 se han asociado con esta neoplasia. OBJETIVO: Evaluar haplotipos de las MMP 7, 8, 12, y 13 y su asociación con CCR. MATERIAL Y MÉTODOS: Se genotipificaron 104 pacientes y 112 individuos sanos mediante reacción en cadena de la polimerasa con análisis del polimorfismo de los fragmentos de restricción (PCR-RFLP). Para el análisis de asociación fueron calculados valores de odds ratio e intervalo de confianza. El análisis de haplotipos y desequilibrio de ligamiento (LD) se realizó con el software Arlequin v3.5. RESULTADOS: Se presentó LD entre rs2276109 y rs2252070. Los haplotipos rs11568818(A)-rs11225395(T)-rs2276109(A)-rs2252070(A) y rs11568818(A)-rs11225395(C)-rs2276109(A)-rs2252070(G) se asociaron con riesgo de CCR y los haplotipos rs11568818(G)-rs11225395(C)-rs2276109(A)-rs2252070(A) y rs11568818(A)-rs11225395(T)-rs2276109(A)-rs2252070(G) con protección. CONCLUSIÓN: Las variantes rs2276109 y rs2252070 mostraron ligamiento génico. Dos haplotipos fueron asociados con el desarrollo de CCR (ATAA y ACAG) y dos fueron asociados con protección (GCAA y ATAG). Este estudio representa el primer reporte de frecuencias de las variantes rs11225395 y rs2276109 en población mexicana.

Sickle cell disease in western Sudan: genetic epidemiology and predictors of knowledge attitude and practices.

OBJECTIVE: To investigate the epidemiology of sickle cell disease (SCD) and determinants of knowledge, attitudes and practices (KAP) towards SCD in western Kordofan State, Sudan. METHODS: A community-based, descriptive, cross-sectional study was conducted in three towns. Three hundred and seventy-two households were polled, and blood samples for haemoglobin phenotyping were collected from 1116 individuals. Sociodemographic, socio-economic and KAP data were collected using investigator-administered questionnaires. Descriptive, frequency distribution and multiple regression analyses were performed. RESULTS: About 50.9% of the study population were Misseriya tribes. Consanguineous marriages were reported by 67.5% of the households. The highest percentage of homozygous SCD was 2.8% among children under 5 years of age. About 24.9% were carriers of HbS allele (HbAS). HbS allele frequency was highest in children aged 5-11 years (18.3%, CI: 13.7-22.9%) and lowest in males >15 years old (12.0%, CI: 6.1-17.9%). The average HbS frequency across all age groups was 14.5% (95% CI: 12.2-16.8%). The most frequent ß-globin gene cluster haplotype was the Cameroon (30.8%), followed by the Benin (21.8%), the Senegal (12.8%) and the Bantu (2.2%) haplotypes. About 17.0% of all-cause child deaths were due to SCD. The estimated change in log odds of having the SS genotype per year increase in age was (-) 0.0058 (95% CI -0.0359, 0.0242). This represents a non-statistically significant 2.9% increase in 5-year mortality for individuals with the SS genotype relative to those with AS and AA genotypes. About 46.9% of the households had poor knowledge, 26.1% had satisfactory knowledge, and 26.9% had good knowledge about sickle cell disease. Mothers' and fathers' educational levels were significant predictors of good knowledge about SCD (P < 0.05). About 48.0% had a satisfactory attitude towards sickle cell disease while 30.7% had poor attitude and only 21.3 showed good attitudes. Poor knowledge about SCD and low socio-economic status were the strongest positive predictors of poor attitude and practices towards SCD (P < 0.01). CONCLUSIONS: Sickle cell disease is a major health problem in West Kordofan, Sudan. Knowledge, attitude and practices towards the disease are not satisfactory. The development of public health programs is highly recommended to control and manage SCD in western parts of Sudan.

Low MBL-associated serine protease 2 (MASP-2) levels correlate with urogenital schistosomiasis in Nigerian children.

OBJECTIVES: The human mannose-binding lectin (MBL) and ficolins (FCN) are involved in pathogen recognition in the first line of defence. They support activation of the complement lectin cascade in the presence of MBL-associated serine protease 2 (MASP-2), a protein that cleaves the C4 and C2 complement components. Recent studies found that distinct MBL2 and FCN2 promoter variants and their corresponding serum levels are associated with relative protection from urogenital schistosomiasis. METHODS: We investigated the contribution of MASP-2 levels and MASP2 polymorphisms in a Nigerian study group, of 163 individuals infected with Schistosoma haematobium and 183 healthy subjects. RESULTS: MASP-2 serum levels varied between younger children (≤12 years) and older children (>12 years) and adults (P = 0.0001). Younger children with a patent infection had significantly lower MASP-2 serum levels than uninfected children (P = 0.0074). Older children and adults (>12 years) with a current infection had higher serum MASP-2 levels than controls (P = 0.032). MBL serum levels correlated positively with MASP-2 serum levels (P = 0.01). MASP2 secretor haplotypes were associated with MASP-2 serum levels in healthy subjects. The heterozygous MASP2 p.P126L variant was associated with reduced serum MASP-2 levels (P = 0.01). CONCLUSIONS: The findings indicate that higher MASP-2 serum levels are associated with relative protection from urogenital schistosomiasis in Nigerian children.

ABCB1 gene variants as risk factors and modulators of age of onset of demyelinating disease in Mexican patients.

INTRODUCTION: The C1236T, G2677T/A, and C3435T variants of the ABCB1 gene alter the functioning of P-glycoprotein and the transport of endogenous and exogenous substances across the blood-brain barrier, and act as risk factors for some neurodegenerative diseases. This study aimed to determine the association between demyelinating disease and the C1236T, G2677T/A, and C3435T variants of ABCB1 and its haplotypes and combinations of genotypes. METHODS: Polymerase chain reaction with restriction fragment length polymorphism analysis (PCR-RFLP) and Sanger sequencing were used to genotype 199 patients with demyelinating disease and 200 controls, all Mexicans of mixed race; frequencies of alleles, genotypes, haplotypes, and genotype combinations were compared between patients and controls. We conducted a logistic regression analysis and calculated chi-square values and 95% confidence intervals (CI); odds ratios (OR) were calculated to evaluate the association with demyelinating disease. RESULTS: The TTT and CGC haplotypes were most frequent in both patients and controls. The G2677 allele was associated with demyelinating disease (OR: 1.79; 95% CI, 1.12-2.86; P =  .015), as were the genotypes GG2677 (OR: 2.72; 95% CI, 1.11-6.68; P =  .025) and CC3435 (OR: 1.82; 95% CI, 1.15-2.90; P =  .010), the combination GG2677/CC3435 (OR: 2.02; 95% CI, 1.17-3.48; P =  .010), and the CAT haplotype (OR: 0.21; 95% CI, 0.05-0.66; P =  .001). TTTTTT carriers presented the earliest age of onset (23.0 ±â€¯7.7 years, vs 31.6 ±â€¯10.7; P =  .0001). CONCLUSIONS: The GG2677/CC3435 genotype combination is associated with demyelinating disease in this sample, particularly among men, who may present toxic accumulation of P-glycoprotein substrates. In our study, the G2677 allele of ABCB1 may differentially modulate age of onset of demyelinating disease in men and women.

ABCB1 gene variants as risk factors and modulators of age of onset of demyelinating disease in Mexican patients. / Variantes del gen ABCB1 como factores de riesgo y factores moduladores de la edad de inicio en pacientes mexicanos con enfermedad desmielinizante.

INTRODUCTION: The C1236T, G2677T/A, and C3435T variants of the ABCB1 gene alter the functioning of P-glycoprotein and the transport of endogenous and exogenous substances across the blood-brain barrier, and act as risk factors for some neurodegenerative diseases. This study aimed to determine the association between demyelinating disease and the C1236T, G2677T/A, and C3435T variants of ABCB1 and its haplotypes and combinations of genotypes. METHODS: Polymerase chain reaction with restriction fragment length polymorphism analysis (PCR-RFLP) and Sanger sequencing were used to genotype 199 patients with demyelinating disease and 200 controls, all Mexicans of mixed race; frequencies of alleles, genotypes, haplotypes, and genotype combinations were compared between patients and controls. We conducted a logistic regression analysis and calculated chi-square values and 95% confidence intervals (CI); odds ratios (OR) were calculated to evaluate the association with demyelinating disease. RESULTS: The TTT and CGC haplotypes were most frequent in both patients and controls. The G2677 allele was associated with demyelinating disease (OR: 1.79; 95% CI: 1.12-2.86; P=.015), as were the genotypes GG2677 (OR: 2.72; 95% CI: 1.11-6.68; P=.025) and CC3435 (OR: 1.82; 95% CI: 1.15-2.90; P=.010), the combination GG2677/CC3435 (OR: 2.02; 95% CI, 1.17-3.48; P=.010), and the CAT haplotype (OR: 0.21; 95% CI: 0.05-0.66; P=.001). TTTTTT carriers presented the earliest age of onset (23.0±7.7 years, vs. 31.6±10.7; P=.0001). CONCLUSIONS: The GG2677/CC3435 genotype combination is associated with demyelinating disease in this sample, particularly among men, who may present toxic accumulation of P-glycoprotein substrates. In our study, the G2677 allele of ABCB1 may differentially modulate age of onset of demyelinating disease in men and women.

Variantes del gen ABCB1 como factores de riesgo y factores moduladores de la edad de inicio en pacientes mexicanos con enfermedad desmielinizante / ABCB1 gene variants as risk factors and modulators of age of onset of demyelinating disease in Mexican patients

Introducción: Las variantes C1236T, G2677T/A y C3435T del gen ABCB1 alteran la función de la glicoproteína P y el transporte de sustancias endógenas y exógenas en la barrera hematoencefálica; además, actúan como factores de susceptibilidad para algunas enfermedades neurodegenerativas.El objetivo del estudio fue determinar la asociación de polimorfismos ABCB1 (C1236T, G2677T/A y C3435T), sus haplotipos y sus combinaciones de genotipos con la enfermedad desmielinizante.MétodoSe genotipificó a 199 pacientes con enfermedad desmielinizante y a 200 controles mestizos mexicanos mediante PCR-RFLP y secuenciación Sanger para comparar las frecuencias de alelos, genotipos, haplotipos y combinaciones de genotipos entre pacientes y controles. El análisis estadístico se realizó con regresión logística y χ2 de Pearson al 95% de confianza; se calculó la OR y se evaluó la asociación con enfermedad desmielinizante.ResultadosLos haplotipos TTT y CGC fueron los más frecuentes en pacientes y controles. El alelo G2677 (OR = 1,79; IC 95%: 1,12-2,86; p = 0,015) muestra asociación con enfermedad desmielinizante, así como los genotipos GG2677 (OR = 2,72; IC 95% = 1,11-6,68; p = 0,025) y CC3435 (OR = 1,82; IC 95%: 1,15-2,90; p = 0,010) y su combinación GG2677/CC3435 (OR = 2,02; IC 95%: 1,17-3,48; p = 0,010) y el haplotipo CAT (OR = 0,21; IC 95%: 0,05-0,66; p = 0,001).Los portadores TTTTTT presentaron la edad de inicio más temprana (23,0 ± 7,7 vs. 31,6 ± 10,7; p = 0,0001).ConclusionesLa combinación de genotipos GG2677/CC3435 está asociada al desarrollo de enfermedad desmielinizante en esta muestra, principalmente en el sexo masculino, en el cual puede darse acumulación tóxica de sustratos de glicoproteína P.En este estudio, la edad de inicio de la enfermedad desmielinizante podría ser modulada diferencialmente entre sexos por el alelo G2677 del gen ABCB1. (AU)

Introduction: The C1236T, G2677T/A, and C3435T variants of the ABCB1 gene alter the functioning of P-glycoprotein and the transport of endogenous and exogenous substances across the blood-brain barrier, and act as risk factors for some neurodegenerative diseases.This study aimed to determine the association between demyelinating disease and the C1236T, G2677T/A, and C3435T variants of ABCB1 and its haplotypes and combinations of genotypes.MethodsPolymerase chain reaction with restriction fragment length polymorphism analysis (PCR-RFLP) and Sanger sequencing were used to genotype 199 patients with demyelinating disease and 200 controls, all Mexicans of mixed race; frequencies of alleles, genotypes, haplotypes, and genotype combinations were compared between patients and controls. We conducted a logistic regression analysis and calculated chi-square values and 95% confidence intervals (CI); odds ratios (OR) were calculated to evaluate the association with demyelinating disease.ResultsThe TTT and CGC haplotypes were most frequent in both patients and controls. The G2677 allele was associated with demyelinating disease (OR: 1.79; 95% CI: 1.12-2.86; P = .015), as were the genotypes GG2677 (OR: 2.72; 95% CI: 1.11-6.68; P = .025) and CC3435 (OR: 1.82; 95% CI: 1.15-2.90; P = .010), the combination GG2677/CC3435 (OR: 2.02; 95% CI, 1.17-3.48; P = .010), and the CAT haplotype (OR: 0.21; 95% CI: 0.05-0.66; P = .001).TTTTTT carriers presented the earliest age of onset (23.0 ± 7.7 years, vs. 31.6 ± 10.7; P = .0001).ConclusionsThe GG2677/CC3435 genotype combination is associated with demyelinating disease in this sample, particularly among men, who may present toxic accumulation of P-glycoprotein substrates.In our study, the G2677 allele of ABCB1 may differentially modulate age of onset of demyelinating disease in men and women. (AU)

Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine / Caracterização fenotípica e molecular de isolados de Pseudomonas aeruginosa resistentes a fluoroquinolonas na Palestina

Fluoroquinolones are important antimicrobial agents for the treatment of Pseudomonas infections. A total of 11 isolates of P. aeruginosa were collected from different clinical samples from different medical centers in the North West Bank-Palestine during 2017. In this study, resistance to fluoroquinolones and secretions of ß-lactamases were detected by phenotypic methods, while presence of ß-lactamase gene sequences and other virulence factors were detected by PCR technique. PCR product for gyrA, parC and parE genes were sequenced for further analyses. The phylogenetic analyses, population diversity indices and haplotypes determination were conducted using computer programs MEGA version 6, DnaSP 5.1001 and median-joining algorithm in the program Network 5, respectively. Results of this study showed that the MIC for ciprofloxacin and norfloxacin had a range of 32-256 µg/ml. In addition, all isolates carried either exoT or exoT and exoY genes, different ß-lactamase genes and 82% of these isolates harbored class 1 integrons. Analyses of the gyrA, parC and parE sequences were found to be polymorphic, had high haplotype diversity (0.945-0.982), low nucleotide diversity (0.01225-0.02001) and number of haplotypes were 9 for each gyrA and parE genes and 10 haplotypes for parC gene. The founder haplotypes being Hap-1 (18%), Hap-2 (27.3%) and Hap-6 (9.1%) for gyrA, parC and parE genes, respectively. Two of ParE haplotypes were detected as indel haplotypes. The Median-joining- (MJ) networks constructed from haplotypes of these genes showed a star-like expansion. The neutrality tests (Tajima's D test and Fu's Fs test) for these genes showed negative values. Palestinian fluoroquinolone resistant P. aeruginosa strains showed high MIC level for fluoroquinolones, ß-lactamase producers, carried type III secretion exotoxin-encoding genes, most of them had integrase I gene and had high level of mutations in QRDR regions in gyrA, parC and parE genes. All these factors may play an important role in the invasiveness of these strains and make them difficult to treat. Isolation of these strains from different medical centers, indicate the need for a strict application of infection control measures in Medical centers in the North West Bank-Palestine that aim to reduce expense and damage caused by P. aeruginosa infections. Molecular analyses showed that Palestinian fluoroquinolone resistant P. aeruginosa haplotypes are not genetically differentiated; however, more mutations may exist in these strains.

Fluoroquinolonas são agentes antimicrobianos importantes para o tratamento de infecções por Pseudomonas. Um total de 11 bacilos isolados de P. aeruginosa foram coletados de diferentes amostras clínicas provenientes de diferentes centros médicos na Cisjordânia-Palestina durante o ano de 2017. Neste estudo, resistência a fluoroquinolonas e secreções de ß-lactamases foram detectadas por métodos fenotípicos, enquanto a presença de sequências do gene ß-lactamase e outros fatores de virulência foram detectados pela técnica de PCR (Proteína C-reativa). O produto de PCR para os genes gyrA, parC e parE foram sequenciados para análises posteriores. As análises filogenéticas, os índices de diversidade populacional e a determinação de haplótipos foram realizados utilizando os softwares MEGA versão 6, DnaSP 5.1001 e o algoritmo de junção de mediana do programa Network 5, respectivamente. Os resultados deste estudo mostraram que a MIC para ciprofloxacina e norfloxacina tinha um intervalo de 32-256 µg/ml. Além disso, todos os bacilos isolados carregavam genes exoT ou exoT e exoY, genes de ß-lactamase diferentes e 82% desses isolados continham integrons de classe 1. As análises das sequências gyrA, parC e parE foram consideradas polimórficas, com alta diversidade de haplótipos (0,945-0,982), baixa diversidade de nucleotídeos (0,01225-0,02001) e o número de haplótipos foi de 9 para cada gene de gyrA e parE e 10 haplótipos para o gene parC. Os haplótipos fundadores são Hap-1 (18%), Hap-2 (27,3%) e Hap-6 (9,1%) para os genes gyrA, parC e parE, respectivamente. Dois dos haplótipos parE foram detectados como haplótipos InDel. As redes Median-joining (MJ) construídas a partir de haplótipos desses genes mostraram uma expansão semelhante à de uma estrela. Os testes de neutralidade (teste D de Tajima e teste Fs de Fu) para esses genes apresentaram valores negativos. As cepas palestinas de P. aeruginosa resistentes a fluoroquinolonas mostraram alto nível de MIC para fluoroquinolonas, produtores de ß-lactamase, genes codificadores de exotoxina de secreção tipo III, a maioria deles tinha o gene integrase I e tinha alto nível de mutações nas regiões QRDR nos genes gyrA, parC e parE. Todos esses fatores podem desempenhar um papel importante na invasão dessas cepas e torná-las difíceis de tratar. O isolamento dessas cepas em diferentes centros médicos, indica a necessidade de uma aplicação estrita de medidas de controle de infecção em centros médicos da Cisjordânia-Palestina que visam reduzir despesas e danos causados por infecções por P. aeruginosa. As análises moleculares mostraram que os haplótipos de P. aeruginosa resistentes à fluoroquinolona palestina não são geneticamente diferenciados; no entanto, mais mutações podem existir nessas cepas.

Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine / Caracterização fenotípica e molecular de isolados de Pseudomonas aeruginosa resistentes a fluoroquinolonas na Palestina

Fluoroquinolones are important antimicrobial agents for the treatment of Pseudomonas infections. A total of 11 isolates of P. aeruginosa were collected from different clinical samples from different medical centers in the North West Bank-Palestine during 2017. In this study, resistance to fluoroquinolones and secretions of β-lactamases were detected by phenotypic methods, while presence of β-lactamase gene sequences and other virulence factors were detected by PCR technique. PCR product for gyrA, parC and parE genes were sequenced for further analyses. The phylogenetic analyses, population diversity indices and haplotypes determination were conducted using computer programs MEGA version 6, DnaSP 5.1001 and median-joining algorithm in the program Network 5, respectively. Results of this study showed that the MIC for ciprofloxacin and norfloxacin had a range of 32-256 µg/ml. In addition, all isolates carried either exoT or exoT and exoY genes, different β-lactamase genes and 82% of these isolates harbored class 1 integrons. Analyses of the gyrA, parC and parE sequences were found to be polymorphic, had high haplotype diversity (0.945-0.982), low nucleotide diversity (0.01225-0.02001) and number of haplotypes were 9 for each gyrA and parE genes and 10 haplotypes for parC gene. The founder haplotypes being Hap-1 (18%), Hap-2 (27.3%) and Hap-6 (9.1%) for gyrA, parC and parE genes, respectively. Two of ParE haplotypes were detected as indel haplotypes. The Median-joining- (MJ) networks constructed from haplotypes of these genes showed a star-like expansion. The neutrality tests (Tajima’s D test and Fu’s Fs test) for these genes showed negative values. Palestinian fluoroquinolone resistant P. aeruginosa strains showed high MIC level for fluoroquinolones, β-lactamase producers, carried type III secretion exotoxin-encoding genes, most of them [...].

Fluoroquinolonas são agentes antimicrobianos importantes para o tratamento de infecções por Pseudomonas. Um total de 11 bacilos isolados de P. aeruginosa foram coletados de diferentes amostras clínicas provenientes de diferentes centros médicos na Cisjordânia-Palestina durante o ano de 2017. Neste estudo, resistência a fluoroquinolonas e secreções de β-lactamases foram detectadas por métodos fenotípicos, enquanto a presença de sequências do gene β-lactamase e outros fatores de virulência foram detectados pela técnica de PCR (Proteína C-reativa). O produto de PCR para os genes gyrA, parC e parE foram sequenciados para análises posteriores. As análises filogenéticas, os índices de diversidade populacional e a determinação de haplótipos foram realizados utilizando os softwares MEGA versão 6, DnaSP 5.1001 e o algoritmo de junção de mediana do programa Network 5, respectivamente. Os resultados deste estudo mostraram que a MIC para ciprofloxacina e norfloxacina tinha um intervalo de 32-256 µg/ml. Além disso, todos os bacilos isolados carregavam genes exoT ou exoT e exoY, genes de β-lactamase diferentes e 82% desses isolados continham integrons de classe 1. As análises das sequências gyrA, parC e parE foram consideradas polimórficas, com alta diversidade de haplótipos (0,945-0,982), baixa diversidade de nucleotídeos (0,01225-0,02001) e o número de haplótipos foi de 9 para cada gene de gyrA e parE e 10 haplótipos para o gene parC. Os haplótipos fundadores são Hap-1 (18%), Hap-2 (27,3%) e Hap-6 (9,1%) para os genes gyrA, parC e parE, respectivamente. Dois dos haplótipos parE foram detectados como haplótipos InDel. As redes Median-joining (MJ) construídas a partir de haplótipos desses genes mostraram uma expansão semelhante à de uma estrela. Os testes de neutralidade (teste D de Tajima e teste Fs de Fu) para esses genes apresentaram valores negativos. As cepas palestinas de P. aeruginosa resistentes a fluoroquinolonas mostraram alto nível de MIC para [...].

Phenotypic and molecular characterization of fluoroquinolone resistant Pseudomonas aeruginosa isolates in Palestine

Abstract Fluoroquinolones are important antimicrobial agents for the treatment of Pseudomonas infections. A total of 11 isolates of P. aeruginosa were collected from different clinical samples from different medical centers in the North West Bank-Palestine during 2017. In this study, resistance to fluoroquinolones and secretions of -lactamases were detected by phenotypic methods, while presence of -lactamase gene sequences and other virulence factors were detected by PCR technique. PCR product for gyrA, parC and parE genes were sequenced for further analyses. The phylogenetic analyses, population diversity indices and haplotypes determination were conducted using computer programs MEGA version 6, DnaSP 5.1001 and median-joining algorithm in the program Network 5, respectively. Results of this study showed that the MIC for ciprofloxacin and norfloxacin had a range of 32-256 µg/ml. In addition, all isolates carried either exoT or exoT and exoY genes, different -lactamase genes and 82% of these isolates harbored class 1 integrons. Analyses of the gyrA, parC and parE sequences were found to be polymorphic, had high haplotype diversity (0.945-0.982), low nucleotide diversity (0.01225-0.02001) and number of haplotypes were 9 for each gyrA and parE genes and 10 haplotypes for parC gene. The founder haplotypes being Hap-1 (18%), Hap-2 (27.3%) and Hap-6 (9.1%) for gyrA, parC and parE genes, respectively. Two of ParE haplotypes were detected as indel haplotypes. The Median-joining- (MJ) networks constructed from haplotypes of these genes showed a star-like expansion. The neutrality tests (Tajimas D test and Fus Fs test) for these genes showed negative values. Palestinian fluoroquinolone resistant P. aeruginosa strains showed high MIC level for fluoroquinolones, -lactamase producers, carried type III secretion exotoxin-encoding genes, most of them had integrase I gene and had high level of mutations in QRDR regions in gyrA, parC and parE genes. All these factors may play an important role in the invasiveness of these strains and make them difficult to treat. Isolation of these strains from different medical centers, indicate the need for a strict application of infection control measures in Medical centers in the North West Bank-Palestine that aim to reduce expense and damage caused by P. aeruginosa infections. Molecular analyses showed that Palestinian fluoroquinolone resistant P. aeruginosa haplotypes are not genetically differentiated; however, more mutations may exist in these strains.

Resumo Fluoroquinolonas são agentes antimicrobianos importantes para o tratamento de infecções por Pseudomonas. Um total de 11 bacilos isolados de P. aeruginosa foram coletados de diferentes amostras clínicas provenientes de diferentes centros médicos na Cisjordânia-Palestina durante o ano de 2017. Neste estudo, resistência a fluoroquinolonas e secreções de -lactamases foram detectadas por métodos fenotípicos, enquanto a presença de sequências do gene -lactamase e outros fatores de virulência foram detectados pela técnica de PCR (Proteína C-reativa). O produto de PCR para os genes gyrA, parC e parE foram sequenciados para análises posteriores. As análises filogenéticas, os índices de diversidade populacional e a determinação de haplótipos foram realizados utilizando os softwares MEGA versão 6, DnaSP 5.1001 e o algoritmo de junção de mediana do programa Network 5, respectivamente. Os resultados deste estudo mostraram que a MIC para ciprofloxacina e norfloxacina tinha um intervalo de 32-256 µg/ml. Além disso, todos os bacilos isolados carregavam genes exoT ou exoT e exoY, genes de -lactamase diferentes e 82% desses isolados continham integrons de classe 1. As análises das sequências gyrA, parC e parE foram consideradas polimórficas, com alta diversidade de haplótipos (0,945-0,982), baixa diversidade de nucleotídeos (0,01225-0,02001) e o número de haplótipos foi de 9 para cada gene de gyrA e parE e 10 haplótipos para o gene parC. Os haplótipos fundadores são Hap-1 (18%), Hap-2 (27,3%) e Hap-6 (9,1%) para os genes gyrA, parC e parE, respectivamente. Dois dos haplótipos parE foram detectados como haplótipos InDel. As redes Median-joining (MJ) construídas a partir de haplótipos desses genes mostraram uma expansão semelhante à de uma estrela. Os testes de neutralidade (teste D de Tajima e teste Fs de Fu) para esses genes apresentaram valores negativos. As cepas palestinas de P. aeruginosa resistentes a fluoroquinolonas mostraram alto nível de MIC para fluoroquinolonas, produtores de -lactamase, genes codificadores de exotoxina de secreção tipo III, a maioria deles tinha o gene integrase I e tinha alto nível de mutações nas regiões QRDR nos genes gyrA, parC e parE. Todos esses fatores podem desempenhar um papel importante na invasão dessas cepas e torná-las difíceis de tratar. O isolamento dessas cepas em diferentes centros médicos, indica a necessidade de uma aplicação estrita de medidas de controle de infecção em centros médicos da Cisjordânia-Palestina que visam reduzir despesas e danos causados por infecções por P. aeruginosa. As análises moleculares mostraram que os haplótipos de P. aeruginosa resistentes à fluoroquinolona palestina não são geneticamente diferenciados; no entanto, mais mutações podem existir nessas cepas.

Genetic determinants and stroke in children with sickle cell disease.

OBJECTIVE: To verify genetic determinants associated with stroke in children with sickle cell disease (SCD). METHODS: Prospective cohort with 110 children submitted to neonatal screening by the Neonatal Screening Program, between 1998 and 2007, with SCD diagnosis, followed at a regional reference public service for hemoglobinopathies. The analyzed variables were type of hemoglobinopathy, gender, coexistence with alpha thalassemia (α-thal), haplotypes of the beta globin chain cluster, and stroke. The final analysis was conducted with 66 children with sickle cell anemia (SCA), using the chi-squared test in the program SPSS® version 14.0. RESULTS: Among children with SCD, 60% had SCA. The prevalence of coexistence with α-thal was 30.3% and the Bantu haplotype (CAR) was identified in 89.2%. The incidence of stroke was significantly higher in those with SCA (27.3% vs. 2.3%; p=0.001) and males (24.1% vs. 9.6%; p=0.044). The presence of α-thal (p=0.196), the CAR haplotype (p=0.543), and socioeconomic factors were not statistically significant in association with the occurrence of stroke. CONCLUSION: There is a high incidence of stroke in male children and in children with SCA. Coexistence with α-thal and haplotypes of the beta globin chain cluster did not show any significant association with stroke. The heterogeneity between previously evaluated populations, the non-reproducibility between studies, and the need to identify factors associated with stroke in patients with SCA indicate the necessity of conducting further research to demonstrate the relevance of genetic factors in stroke related to SCD.

CO1-Based DNA barcoding for assessing diversity of Pteropus giganteus from the state of Azad Jammu Kashmir, Pakistan / Código de barras de DNA à base de CO1 para avaliar a diversidade de Pteropus giganteus do estado de Azad Jammu e Caxemira, Paquistão

Abstract The flying fox (Pteropus giganteus) also familiar with the name of the greater Indian fruit Bat belongs to the order Chiroptera and family Pteropodidae. Current research emphasis on the DNA barcoding of P. giganteus in Azad Jammu Kashmir. Bat sequences were amplified and PCR products were sequenced and examined by bioinformatics software. Congeneric and conspecific, nucleotide composition and K2P nucleotide deviation, haplotype diversity and the number of haplotypes were estimated. The analysis showed that all of the five studied samples of P. giganteus had low G contents (G 19.8%) than C (27.8%), A (25.1%) and T (27.3%) contents. The calculated haplotype diversity was 0.60% and the mean intraspecific K2P distance was 0.001% having a high number of transitional substitutions. The study suggested that P. giganteus (R=0.00) do not deviate from the neutral evolution. It was determined from the conclusion that this mtDNA gene is a better marker for identification of Bat species than nuclear genes due to its distinctive characteristics and may serve as a landmark for the identification of interconnected species at the molecular level and in the determination of population genetics.

Resumo A raposa-voadora (Pteropus giganteus), também conhecida como morcego indiano, pertence à ordem dos Chiroptera e à família Pteropodidae. A presente pesquisa dá ênfase ao código de barras de DNA de P. giganteus em Azad Jammu e Caxemira. Sequências genéticas dos morcegos foram amplificadas, e os produtos de PCR foram sequenciados e examinados por software de bioinformática. De espécies congenérica e coespecífica, foram estimados composição nucleotídica e desvio de nucleotídeos K2P, diversidade de haplótipos e número de haplótipos. A análise mostrou que todas as cinco amostras estudadas de P. giganteus apresentaram baixos teores de G (19,8%) em comparação com C (27,8%), A (25,1%) e T (27,3%). A diversidade de haplótipos calculada foi de 0,60%, e a distância média intraespecífica de K2P foi de 0,001%, com um elevado número de substituições transicionais. O estudo sugeriu que P. giganteus (R = 0,00) não se desviou da evolução neutra. É possível concluir que o gene mtDNA é um marcador favorável para identificação de espécies de morcegos do que genes nucleares por causa de suas características distintivas e pode servir como um marco para a identificação de espécies interconectadas em nível molecular e para a determinação genética de populações.

Identification of patterns related to linkage groups or disequilibrium by factor analysis / Identificação de padrões relacionados a grupos de ligação ou de desequilíbrio por análise de fatores

ABSTRACT: Empirical patterns of linkage disequilibrium (LD) can be used to increase the statistical power of genetic mapping. This study was carried out with the objective of verifying the efficacy of factor analysis (AF) applied to data sets of molecular markers of the SNP type, in order to identify linkage groups and haplotypes blocks. The SNPs data set used was derived from a simulation process of an F2 population, containing 2000 marks with information of 500 individuals. The estimation of the factorial loadings of FA was made in two ways, considering the matrix of distances between the markers (A) and considering the correlation matrix (R). The number of factors (k) to be used was established based on the graph scree-plot and based on the proportion of the total variance explained. Results indicated that matrices A and R lead to similar results. Based on the scree-plot we considered k equal to 10 and the factors interpreted as being representative of the bonding groups. The second criterion led to a number of factors equal to 50, and the factors interpreted as being representative of the haplotypes blocks. This showed the potential of the technique, making it possible to obtain results applicable to any type of population, helping or corroborating the interpretation of genomic studies. The study demonstrated that AF was able to identify patterns of association between markers, identifying subgroups of markers that reflect factor binding groups and also linkage disequilibrium groups.

RESUMO: Padrões empíricos de desequilíbrio de ligação (LD) podem ser utilizados para aumentar o poder estatístico do mapeamento genético. Este trabalho foi realizado com o objetivo de verificar a eficácia da análise de fatores (AF) aplicada a conjuntos de dados de marcadores moleculares do tipo SNP, visando identificar grupos de ligação e blocos de haplótipos. O conjunto de dados SNPs utilizado foi oriundo de um processo de simulação de uma população F2, contendo 2000 marcas com informações de 500 indivíduos. A estimação das cargas fatoriais (loadings) da AF foi feita de duas formas, considerando a matriz de distâncias entre os marcadores (A) e considerando a matriz de correlação (R). O número de fatores (k) a ser utilizado foi estabelecido com base no gráfico scree-plot e com base na proporção da variância total explicada. Os resultados indicam que as matrizes A e R conduzem a resultados similares. Com base no scree-plot considerou-se k igual a 10 e os fatores interpretados como sendo representativos dos grupos de ligação. O segundo critério conduziu a um número de fatores igual a 50, e os fatores interpretados como sendo representativos dos blocos de haplótipos. Isto mostra o potencial da técnica que permite obter resultados aplicáveis ​​a qualquer tipo de população, corroborando a interpretação de estudos genômicos. O trabalho demonstrou que a AF foi capaz de identificar padrões de associação entre marcadores, identificando subgrupos de marcadores que refletem grupos de ligação fatorial e também grupos de desequilíbrio de ligação.

Lethal and semi-lethal mutations in Holstein calves in Uruguay / Mutações letais e semi-letais em bezerros da raça Holandesa no Uruguai

ABSTRACT: Genetic disorders in Holstein cattle are a health problem that has grown worldwide in recent years, compromising the sustainability of modern dairy production. In Uruguay, Holstein-based milk production is one of the most important sectors of the country's economy, but high levels of inbreeding have decreased the breed's fertility in recent decades. This study investigated the presence and diffusion of lethal and semi-lethal alleles causing embryo death, abortions, fetal malformations, and neonatal diseases in Holstein calves. Using the GeneSeek® Genomic Profiler™ Bovine 50K BeadChip, we genotyped 383 calves (1-30 days-old) from 27 farms located in the main dairy region of Uruguay. Results showed a high prevalence of farms (85%) and carrier calves (21%), including one or more of the following semi-lethal or lethal alleles: Syndactylism (4.18%), brachyspina (3.39%), cholesterol deficiency haplotype (2.61%), complex vertebral malformation (2.09%), bovine leukocyte adhesion deficiency (1.04%s), and Holstein haplotypes HH1 (4.44%), HH3 (3.13%), HH4 (1.04%), and HH5 (0.26%). Most of these alleles had not been recognized previously in Uruguay. We concluded that lethal and semi-lethal mutations are widespread in the Holstein breed in Uruguay. More studies are required to determine their impact on dairy cattle fertility.

RESUMO: Os distúrbios genéticos nos bovinos da raça Holandesa são um problema de saúde que cresceu nos últimos anos a nível mundial, comprometendo a sustentabilidade da produção leiteira moderna. No Uruguai, a produção leiteira com base na raça Holstein é um dos setores mais importantes da economia do país, mas altos níveis de endogamia diminuíram a fertilidade da raça nas últimas décadas. O objetivo deste estudo foi investigar a presença e difusão de alelos letais e semi-letais causando morte de embriões, abortos, malformações fetais e doenças neonatais em bezerros da raça Holandesa. Usando o BeadChip Bovino 50K GeneSeek® Genomic Profiler™, genotipamos 383 bezerros (menos de um mês) de 27 fazendas localizadas na principal região leiteira do Uruguai. Os resultados mostraram uma alta prevalência de fazendas (85%) e bezerros portadores (21%), incluindo um ou mais dos seguintes alelos letais ou semi-letais: sindactilismo (4,18%), braquipespina (3,39%), haplótipo de deficiência de colesterol (2,61%), malformação vertebral complexa (2,09%), deficiência de adesão de leucócitos bovinos (1,04% s) e haplótipos de Holstein HH1 (4,44%), HH3 (3,13%), HH4 (1,04%) e HH5 (0,26%). A maioria desses alelos não havia sido reconhecida anteriormente no país. Concluímos que as mutações letais e semi-letais são comuns na raça Holstein no Uruguai. Mais estudos são necessários para determinar seu impacto na fertilidade do gado leiteiro.

Estructura genética de cepas de Mycobacterium tuberculosis farmacorresistentes en Perú con base en haplotipos obtenidos de un ensayo de sonda lineal / Genetic structure of drug-resistant strains of Mycobacterium tuberculosis in Peru based on haplotypes obtained from a linear probe assay

RESUMEN Objetivo. Determinar la estructura genética de las cepas drogorresistentes de Mycobacterium tuberculosis que circularon en todo el Perú durante los años 2011-2015 a través de haplotipos obtenidos de un ensayo con sondas en línea. Materiales y métodos. Se analizaron 6589 muestras que ingresaron al Instituto Nacional de Salud para el diagnóstico rutinario mediante el ensayo GenoType® MTBDRplus v2, durante el periodo de estudio. Se crearon haplotipos resistentes mediante la concatenación de 21 sitios polimórficos de los genes evaluados por el ensayo con sondas en línea, y se realizó el análisis de asociación con fenotipos obtenidos por el método de proporciones agar 7H10. Resultados. Las mutaciones de mayores frecuencias fueron: rpoB S531L (55,4%) y rpoB D516V (18,5%) para la resistencia a rifampicina, y katG S315T (59,5%) e inhA c-15t (25,7%) para la resistencia a isoniacida. Se obtuvieron 13 haplotipos representativos (87,8% de muestras analizadas) de los cuales seis correspondieron al genotipo multidrogorresistente, cuatro al genotipo monorresistente a isoniacida y tres al genotipo monorresistente a rifampicina. Dieciocho departamentos, y la provincia del Callao, presentaron una alta diversidad haplotípica; cuatro presentaron moderada diversidad y dos presentaron baja diversidad. Conclusiones. Existe una alta diversidad haplotípica en la mayoría de los departamentos, además de una concentración de las cepas de Mycobacterium tuberculosis drogorresistentes en las ciudades de Lima y Callao. Asimismo, las cepas de Mycobacterium tuberculosis con perfil drogorresistente que circulan en el Perú contienen principalmente los marcadores genéticos de mayor prevalencia a nivel mundial asociados con la resistencia frente a rifampicina e isoniacida.

ABSTRACT Objective. To determine the genetic structure of drug-resistant strains of Mycobacterium tuberculosis that circulated throughout Peru during the years 2011-2015, by using haplotypes obtained from a line probe assay. Materials and methods. A total of 6589 samples that were admitted to the Instituto Nacional de Salud for routine diagnosis using the GenoType® MTBDRplus v2 assay were analyzed during the study period. Resistant haplotypes were created by concatenating 21 polymorphic sites of the evaluated genes using the line probe assay; and the association analysis was carried out with phenotypes obtained by the 7H10 agar ratio method. Results. The most frequent mutations were: rpoB S531L (55.4%) and rpoB D516V (18.5%) for rifampicin resistance, and katG S315T (59.5%) and inhA c-15t (25.7%) for isoniazid resistance. We obtained 13 representative haplotypes (87.8% of analyzed samples), 6 corresponded to the multidrug-resistant genotype, 4 to the isoniazid mono-resistant genotype and 3 to the rifampicin mono-resistant genotype. Eighteen regions and the province of Callao showed high haplotype diversity; four showed moderate diversity and two showed low diversity. Conclusions. Most regions showed high haplotype diversity; in addition, most drug-resistant strains of Mycobacterium tuberculosis were concentrated in the cities of Lima and Callao. Likewise, drug-resistant Mycobacterium tuberculosis strains circulating in Peru mainly contain the genetic markers with the highest prevalence worldwide, which are associated with resistance to rifampicin and isoniazid.

[Association analysis of SNP-63 and indel-19 variant in the calpain-10 gene with polycystic ovary syndrome in women of reproductive age]. / Análisis de asociación del SNP-63 y la variante indel-19 del gen de calpaína-10 con síndrome de ovario poliquístico en mujeres en edad reproductiva.

BACKGROUND: Polycystic ovary syndrome is a complex and heterogeneous disease involving both reproductive and metabolic problems. It has been suggested a genetic predisposition in the etiology of this syndrome. The identification of calpain-10 gene (CAPN10) as the first candidate gene for type 2 diabetes mellitus, has focused the interest in investigating their possible relation with the polycystic ovary syndrome, because this syndrome is associated with hyperinsulinemia and insulin resistance, two metabolic abnormalities associated with type 2 diabetes mellitus. OBJECTIVE: To investigate if there is association between the SNP-63 and the variant indel-19 of the CAPN10 gene and polycystic ovary syndrome in women of reproductive age. MATERIAL AND METHODS: This study included 101 women (55 with polycystic ovary syndrome and 46 without polycystic ovary syndrome). The genetic variant indel-19 was identified by electrophoresis of the amplified fragments by PCR, and the SNP-63 by PCR-RFLP. RESULTS: The allele and genotype frequencies of the two variants do not differ significatly between women with polycystic ovary syndrome and control women group. The haplotype 21 (defined by the insertion allele of indel-19 variant and C allele of SNP-63) was found with higher frequency in both study groups, being more frequent in the polycystic ovary syndrome patients group, however, this difference was not statistically significant (p = 0.8353). CONCLUSIONS: The results suggest that SNP-63 and indel-19 variant of the CAPN10 gene do not represent a risk factor for polycystic ovary syndrome in our patients group.

Genotipos de Echinococcus granulosus en hidatidosis humana alrededor del mundo: revisión sistemática / Echinococcus granulosus genotypes verified in human hydatid disease around the world: systematic review

Resumen Introducción: La evidencia sobre las características genotípicas de la infección por Echinococcus granulosus en humanos es escasa. Objetivo: Desarrollar un resumen de la evidencia disponible respecto a genotipos de E. granulosus verificados en hidatidosis humana en el mundo. Material y Métodos: Revisión sistemática. Se incluyeron artículos relacionados con genotipos de E. granulosus, en humanos, sin restricción de lenguaje ni método de secuenciación; publicados entre 1990-2019. Se realizó una búsqueda sistemática en WoS, EMBASE, MEDLINE, SCOPUS, Trip Database, BIREME, SciELO, LILACS, IBECS y OPS-OMS. Las variables en estudio fueron: año de publicación, país de origen, número de muestras, órganos parasitados, marcador molecular utilizado y genotipo identificado. Se aplicó estadística descriptiva. Resultados: Se identificaron 701 artículos relacionados; 62 cumplieron los criterios de selección, representando 1.511 muestras. La evidencia existente fue publicada entre 1994 y 2019 y proviene principalmente de Irán (45,2%). El método de secuenciación más utilizado fue amplificación por reacción de polimerasa en cadena más secuenciación tipo Sanger con genotipificación del gen cox1 (79,0%). Los genotipos identificados con mayor frecuencia fueron G1 (49,1%) y el complejo G1/G3 (32,2%). Conclusión: Las publicaciones relacionadas con genotipos de E. granulosus en humanos son escasas y heterogéneas. Eg G1 representa la mayor parte de la carga global mundial.

Abstract Background: The evidence regarding genotypic characteristics of Echinococcus granulosus infection in humans worldwide is scarce. Aim: To develop a synthesis of the available evidence regarding genotypes of E. granulosus verified in humans worldwide. Methods: Systematic review. Articles related with genotypes of E. granulosus, in humans, without language neither genotyped method restriction, published between 1990-2019 were included. A systematic in WoS, EMBASE, MEDLINE, SCOPUS, Trip Database, BIREME, SciELO, LILACS, IBECS, and PAHO-WHO was carried out. In study variables were year of publication, country, number of samples, host and parasite organs, genotype identified, molecular marker and genes. Descriptive statistics were applied. Results: 701 related articles were identified; 62 fulfilled selection criteria, representing 1,511 samples. The existing evidence was published between 1994 and 2019; and mainly comes from Iran (45.2%). The most commonly used sequencing method was PCR amplification and Sanger type sequencing with partial or total genotyping of the cox1 gene. Genotyped method most frequently used was cox1 (79,0%). Genotypes most frequently identified were G1 and G1/G3 complex (49.1% and 32.2%). Conclusions: Publications related to genotypes of Eg in humans are scarce, heterogeneous, and presenting differing results. Eg G1/G3 accounts for most of the global burden worldwide.

Especies Crípticas Lutzomyia longipalpis (Diptera: Phlebotominae) y sus Implicaciones en la Transmisión de Leishmaniasis en Panamá / Cryptic Species Lutzomy ia longipalpis (Diptera: Phlebotominae) and its Implications in the Transmission of Leishmaniasis in Panama

Lutzomyia longipalpis es el principal v ector de una importante enfermedad desatendida en América. La diversidad genética de este vector se estimó en la población colectada en dos áreas geográficas separadas por hasta 37 km. Analizamos la secuencia CB3­PDR / N1N­PDR de 22 individuos obte­ niendo un parámetro de: h = 0.43 y π = 0.0017 (Bona), h = 0.89, π = 0.004 (El Limón) con una dife­ renciación genética de kst = 0.03; p> 0.05 entre ellos. Ocho haplotipos fueron detectados, de los cuales fue compartido. Se detectó una diferenciación significativa entre las poblaciones Panamá­ Colombia (kst = 0.98), Panamá­Costa Rica (kst = 0.98) y Panamá­Brasil (kst = 0.72) bajo el modelo de aislamiento. Las inferencias genéticas de esta población pueden complementar la información de la capacidad de dispersión y brindar pistas importantes para comprender la ecología de Lutzom­yia longipalpisen Panamá.

Lutzomyia longipalpis is the main vector of an important neglected disease in America. The genetic div ers ity of this vector was estimated in the population collected in two geographical areas separated by up to 37 km. We analyzed the sequence CB3­PDR / N1N­PDR of 22 individuals obtaining a parameter of: h = 0.43 and π = 0.0017 (Bona), h = 0.89, π = 0.004 (The Lemon) with a genetic differentiation of kst = 0.03; p> 0.05 between them. Eight haplotypes were detected, of which it was shared. A significant differentiation was detected between the Panama­Colombia (ks t = 0.98), Panama­Costa Rica (kst = 0.98) and Panama­Brazil (kst = 0.72) populations under the isolation model. The genetic inferences of this population can complement the dispersion information and provide important clues to understand the ecology of Lutzomyia longipalpis in Panama.

LEPR polymorphisms and haplotypes in Mexican patients with colorectal cancer / Polimorfismos y haplotipos del gen LEPR en pacientes mexicanos con cáncer colorrectal

Abstract Introduction: Obesity and colorectal cancer could be linked by adipocytokines, which are proteins associated with cell proliferation. High levels of the adipocytokine leptin promote the development of colorectal cancer through its receptor. Objective: To determine the association between c.326A>G and c.668A>G LEPR gene polymorphisms and colorectal cancer. Materials and methods: DNA was extracted from the peripheral blood of 147 patients with sporadic colorectal cancer and 134 healthy people. Genotypes were obtained by PCR- RFLP and the association was determined by the odds ratio (OR) test using the SPSS™, version 10.0, program. Haplotype frequencies and linkage disequilibrium were estimated by the Arlequin, version 3.5, software. Results: Both polymorphisms were in Hardy-Weinberg equilibrium. Only the c.326A>G heterozygous genotype revealed an increased risk for colorectal cancer development (OR=1.81, 95% CI=1.04-3.16, p=0.04). The AG haplotype showed a significant association with colorectal cancer (OR=0.58, 95% CI=0.35-0.96, p<0.03). Linkage disequilibrium between the variants was only evident for the patients group (r2=0.36). Conclusion: Our results suggest that AG individuals heterozygous for the c.326A>G LEPR variant have a higher risk of colorectal cancer development whereas the AG haplotype (c.326A/c.668G) has a protective effect in the Mexican population.

Resumen Introducción. La relación entre la obesidad y el cáncer colorrectal podría estar dada por las adipocitocinas, proteínas asociadas con la proliferación celular. Los niveles elevados de la adipocitocina leptina promueven el desarrollo del cáncer colorrectal a través de su receptor. Objetivo. Determinar la asociación de los polimorfismos c.326A>G y c.668A>G del gen LEPR con el cáncer colorrectal. Materiales y métodos. A partir de sangre periférica, se extrajo el ADN de 147 pacientes con cáncer colorrectal esporádico y de 134 personas sanas. La genotipificación se hizo mediante PCR-RFLP y la asociación se determinó por la odds ratio (OR) en el programa SPSS™, versión 10.0. Las frecuencias haplotípicas y el desequilibrio de ligamiento se estimaron utilizando el programa Arlequin, versión 3.5. Resultados. Ambos polimorfismos estaban en equilibrio de Hardy-Weinberg. Solo el genotipo heterocigoto c.326A>G reveló un mayor riesgo de desarrollar cáncer colorrectal (OR=1,81; IC95% 1,04-3,16; p=0,04). El haplotipo AG mostró una asociación significativa con este cáncer (OR=0,58; IC95% 0,35-0,96; p≤0,03) y el desequilibrio de ligamiento entre las variantes fue evidente únicamente en el grupo de pacientes (r2=0,36). Conclusión. Los resultados sugieren que los individuos heterocigotos con el haplotipo AG para la variante c.326A>G en el gen LEPR tenían un mayor riesgo de desarrollar cáncer colorrectal, en tanto que el haplotipo AG (c.326A/c.668G) tenía un efecto protector en la población mexicana.

Análisis de la variabilidad genética de una muestra de la población de Bogotá: hacia la constitución de un mapa de haplotipos / Genetic variability analysis in a population from Bogotá: Towards a haplotype map

Resumen Introducción. Los proyectos del mapa de haplotipos (HapMap) y de los 1.000 genomas han sido fundamentales para la compresión del componente genético de las enfermedades comunes y los fenotipos normales. Sin embargo, la variabilidad genética colombiana incluida en estos proyectos no es representativa del país. Objetivo. Contribuir al conocimiento de la variabilidad genética de la población colombiana a partir del estudio genómico de una muestra de individuos de Bogotá. Materiales y métodos. Se genotipificaron 2'372.784 marcadores genéticos de 32 individuos nacidos en Bogotá y de padres originarios de la misma ciudad utilizando la plataforma Illumina™. Los niveles de variabilidad genética se determinaron y se compararon con los datos disponibles de otras poblaciones del proyecto de los 1.000 genomas. Resultados. Los individuos analizados presentaron una variabilidad genética semejante a la de poblaciones con las que comparten ancestros. No obstante, a pesar de la poca diferenciación genética detectada en la población de Bogotá y en la de Medellín, el análisis de los componentes principales sugiere una composición genética diferente en las dos poblaciones. Conclusiones. El análisis genómico de la muestra de Bogotá permitió detectar similitudes y diferencias con otras poblaciones americanas. El aumento de tamaño de la muestra bogotana y la inclusión de muestras de otras regiones del país permitirán una mejor compresión de la variabilidad genética en Colombia, lo cual es fundamental para los estudios de salud humana, y la prevención y el tratamiento de enfermedades comunes en el país.

Abstract Introduction: The HapMap and the 1000 Genomes projects have been important for understanding the genetic component of common diseases and normal phenotypes. However, the Colombian genetic variability included in these projects is not fully representative of our country. Objective: To contribute to the knowledge of the Colombian genetic variability through the genomic study of a sample of individuals from Bogotá. Materials and methods: A total of 2,372,784 genetic markers were genotyped in 32 individuals born in Bogotá whose parents are from the same region, using the Illumina™ platform. The genetic variability levels were determined and compared with the data available from other populations of the 1000 Genomes Project. Results: The genetic variability detected in the individuals from Bogotá was similar to those with shared ancestry. However, despite the low levels of genetic differentiation between Bogotá and Medellín, populations the principal component analysis suggested a different genetic composition in them. Conclusions: Our genomic analysis of a Bogotá sample allowed us to detect similarities and differences with other American populations. The increase of the Bogotá sample and the inclusion of samples from other regions of the country will improve our understanding of the genetic variability in Colombia, essential for studies of human health and the prevention and treatment of common diseases in our country.

Análisis de 27 marcadores STR del cromosoma Y en poblaciones de la selva del Perú / Analysis of 27 STR markers of the chromosome Y in the population of the jungle from Peru

Introducción: los marcadores de repeticiones cortas en tándem del cromosoma Y (Y-STR) se ubican en la región no recombinante del cromosoma Y, su herencia es por vía paterna, no son detectables en el ADN femenino. Estas propiedades hacen de los Y-STR una herramienta útil en las investigaciones forenses, como las agresiones sexuales, paternidades y otros delitos violentos; asimismo son útiles en estudios genealógicos y evolutivos. El objetivo de la investigación es ampliar la evidencia científica de la distribución por regiones o país de los haplotipos del cromosoma sexual Y, estudios similares en poblaciones peruanas son escasas debido al número menor de polimorfismos Y-STR de uso frecuente en genética forense y de poblaciones. Material y métodos: en la investigación se analizaron 141 muestras de ADN de la selva del Perú, de las que 104 muestras corresponden a la región de Iquitos (Loreto), 29 muestras son Awajun (Amazonas) y 8 muestras de Tambopata (Madre de Dios). Las muestras fueron procesadas empleando PCR directa con el kit Yfiler™ Plus PCR Amplification para 27 STR, los productos amplificados fueron analizados por electroforesis capilar en el Applied Biosystem™ 3500XL Genetic Analyzer y los datos obtenidos se importaron al software GeneMapper® ID-X v1.5 para generar los perfiles genéticos. Con los resultados obtenidos se realizó el análisis estadístico y la estructura poblacional. Resultados: de las 141 muestras se obtuvieron 106 haplotipos únicos. La diversidad genética para cada marcador Y-STR estuvo entre 0,317 y 0,919. La diversidad haplotípica para la muestra total fue de 0,9906. El estudio registra que los haplotipos Y-STR estudiados presentaron elevado polimorfismo en la población analizada y, por lo tanto, son de gran utilidad en estudios forenses de identificación humana, así como en genética de poblaciones cuando se investigan grupos o individuos de América Latina. (AU)

Y-chromosome-specific short tandem repeat (Y-STR) markers reside on the non-recombinant portion of the Y chromosome, their inheritance is paternal, they are not detectable in female DNA. These properties make Y-STRs a useful tool in forensic investigations such as sexual assault, parenting, and other violent crimes; likewise they are also useful in genealogical and evolutionary studies. The objective of the research is to expand the scientific evidence of the distribution by region or country of the Y sex chromosome haplotypes. Similar studies in Peruvian populations are scarce due to the smaller number of Y-STR polymorphisms frequently used in Forensic and Population Genetics. Material and method: In the investigation, 141 DNA samples from the jungle of Peru were analyzed, of which comprised of 104 samples from Iquitos region (Loreto), 29 samples from Awajun (Amazonas) and 8 samples from Tambopata (Madre de Dios). The samples were processed using direct PCR with the Yfiler™ Plus PCR Amplification kit for 27 STRs, the amplified products were analyzed by capillary electrophoresis on the Applied Biosystem™ 3500XL Genetic Analyzer, and the data obtained was imported into the GeneMapper® ID-X v1.5 software to generate the genetic profiles. With the results obtained, the statistical analysis and the population structure were carried out. Results: Of the 141 samples, 106 unique haplotypes were observed. Gene diversities for each Y-STR marker ranged from 0.317 to 0.919. The haplotype diversity for the total sample was 0.9906. This study supports that the Y-STR haplotypes in this population are highly polymorphic in the analyzed population and, therefore, are very useful in forensic studies of human identification, as well as in population genetics when investigating groups or individuals from Latin America. (AU)