Potential unreliability of ALK variant allele frequency in the efficacy prediction of targeted therapy in NSCLC / 医学前沿

Anaplastic lymphoma kinase (ALK) is the most common fusion gene involved in non-small cell lung cancer (NSCLC), and remarkable response has been achieved with the use of ALK tyrosine kinase inhibitors (ALK-TKIs). However, the clinical efficacy is highly variable. Pre-existing intratumoral heterogeneity (ITH) has been proven to contribute to the poor treatment response and the resistance to targeted therapies. In this work, we investigated whether the variant allele frequencies (VAFs) of ALK fusions can help assess ITH and predict targeted therapy efficacy. Through the application of next-generation sequencing (NGS), 7.2% (326/4548) of patients were detected to be ALK positive. On the basis of the adjusted VAF (adjVAF, VAF normalization for tumor purity) of four different threshold values (adjVAF < 50%, 40%, 30%, or 20%), the association of ALK subclonality with crizotinib efficacy was assessed. Nonetheless, no statistical association was observed between median progression-free survival (PFS) and ALK subclonality assessed by adjVAF, and a poor correlation of adjVAF with PFS was found among the 85 patients who received first-line crizotinib. Results suggest that the ALK VAF determined by hybrid capture-based NGS is probably unreliable for ITH assessment and targeted therapy efficacy prediction in NSCLC.

Prognostic Predictive Value of ITPKB Mutation's Variant Allele Frequency in Diffuse Large B-cell Lymphoma / 肿瘤防治研究

Objective To investigate the correlation between ITPKB mutation's variant allele frequency (VAF) and prognosis of diffuse large B-cell lymphoma (DLBCL). Methods This study included 155 patients with DLBCL initially diagnosed in the People's Hospital of Xinjiang Uygur Autonomous Region from June 2014 to December 2020. Paraffin-embedded tumor tissue specimens were obtained, and tumor tissue DNA was extracted. A total of 475 hotspot genes including ITPKB were detected by the next generation sequencing to analyze the relationship of the VAF of high-frequency mutant gene with progression-free survival (PFS) and overall survival (OS). Results The mutation frequency of ITPKB was 18.71%. The PFS was significantly shorter in the patients with ITPKB mutations than in those without mutations (37 months vs. 108 months; HR=1.643, 95%CI: 0.920-2.934, P=0.093). The R-language based web tool was used to find the best VAF cutoff to differentiate prognosis. The patients were divided into two groups (VAF High vs. VAF Low+Wt) according to their VAF values. The optimal VAF threshold for ITPKB was 27.48% (HR=3.480, 95%CI: 1.70-7.13, P=0.00027). Multivariate Cox analysis was conducted using clinical indicators such as age, gender, COO classification, IPI, and LDH, and the results showed that PFS was associated with high ITPKB VAF (≥28%) (HR=3.592, 95%CI: 1.738-7.425, P < 0.001) which was an independent adverse predictor of PFS. Conclusion The high load of ITPKB mutation is an independent risk factor for the PFS of patients with DLBCL, and the VAF of ITPKB mutation has a prognostic predictive value for patients with DLBCL.

Frequency of Rh and K antigens in blood donors in Riyadh

ABSTRACT Objectives: Investigate the prevalence of Rh and the K antigens and their phenotypes in the red blood cells of blood donors in Riyadh, Saudi Arabia. Methods: This is a retrospective study. The five principal Rh antigens (D, C, c, E, e) and the Kell antigen from the Kell blood group were tested in 4,675 random samples collected from four blood bank centers in Riyadh. Data were collected for seven weeks (from January 4, 2019 to February 28, 2019). Antigens were tested using the TANGO Optimo system. Results: We found that approximately 86% of the donors had the D antigen, 66% had C, 78% had c, 26% had E, 97% had e and 14% had K. The most common Rh phenotypes were R1r (31%) and R1R1 (22%). Conclusion: The differences in the results between the study population and other populations, such as Caucasian, Indian and African populations indicate the importance of establishing a population-specific database.

Frequency analysis of RHD*1227A allele among Rh negative Han population and random population in Liaoning / 中国输血杂志

【Objective】 To investigate the frequency of RHD*1227A allele in Rh negative Han polulation and random population in Liaoning. 【Methods】 Del phenotype was screened by absorption-elution test, the RHD*1227A allele was screened by PCR-SSP and confirmed by nucleotide sequence analysis of RHD full coding region, and the heterozygosity of RHD gene was detected by hybridization technique. 【Results】 24 case of Del phenotype were detected by the absorption-elution test among 117 Rh negative individuals. 23 RHD*1227A allele carriers were detected by PCR-SSP and sequencing-based typing (SBT). Genotype of 19 individuals was RHD*1227A/RHD*01N.01, while the other 4 was homozygous RHD*1227A/ RHD*1227A.11 individuals were detected as RHD*1227A allele among 1 045 random blood donors, among which 9 were RHD*1227A/RHD*01 and 2 were RHD*1227A/RHD*01N.01. 【Conclusion】 The frequency of RHD*1227A allele is 0.115 4 in Rh negative Han population and 0.005 3 in random population in Liaoning..

Asociación del polimorfismo FecB con la prolificidad natural del Ovino de Pelo Colombiano / Association of the FecB polymorphism with the natural prolificacy of the Colombian Creole Sheep

RESUMEN Objetivo. Caracterizar y asociar el polimorfismo FecB con la prolificidad natural en los biotipos de Ovino de Pelo Colombiano (OPC) Etíope y Sudán. Materiales y métodos. En 300 nacimientos provenientes de 167 ovejas de OPC, de los biotipos, Sudán (n=73) y Etíope (n=94), se midió el efecto del genotipo FecB, y de los factores no genéticos: número de parto de la madre, el padre, la época y el año de concepción, sobre la prolificidad natural (coderos/hembra/parto). Para esto, los animales fueron genotipados por PCR-RFLP (Avail) para FecB y los registros productivos del rebaño fueron analizados. Se calcularon las frecuencias alélicas y genotípicas, las cuales junto con los factores no genéticos fueron asociados a la prolificidad usando un modelo GLM de efectos fijos. Resultados. El alelo FecBB presentó menor frecuencia (0.379±0.152) que el alelo FecB+ (0.622±0.152) para todo el OPC. Estas frecuencias variaron (p<0.05) entre biotipos (Sudán: 0.486, Etíope: 0.271), lo mismo ocurrió con el genotipo FecBBB (0.078 en Etíope y 0.236 en Sudán). El genotipo FecB++ fue más frecuente en Etíope (0.526) y el genotipo heterocigoto en Sudán (0.5) y para el OPC (0.448±0.070). No se encontraron diferencias significativas entre biotipos para los factores no genéticos. La prolificidad varió (p<0.05) entre biotipos (1.45±0.22 en Etíope y 1.34±0.03 en Sudán), con un promedio de 1.40±0.11 para el OPC. Ninguno de los factores no genéticos al igual que los genotipos FecB afectaron la prolificidad natural del OPC (p>0.05). Sin embargo, esta fue más alta en el genotipo FecBBB. Conclusiones. El locus estudiado fue polimórfico. La prolificidad no se afectó por los factores no genéticos ni por el genotipo FecB. Estos resultados podrían ser utilizados en planes de selección asistida para aumentar la productividad del OPC.

ABSTRACT Objective. Characterize and associate the FecB polymorphism with the natural prolificacy in the biotypes of Colombian creole sheep (OPC) Etíope and Sudán. Materials and methods. At 300 births from 167 OPC sheep, from the biotypes, Sudan (n = 73) and Ethiopian (n = 94), the effect of the FecB genotype was measured, and of the non-genetic factors: number of parturitions of the mother, the father, the season and the year of conception, on the natural prolificacy (litter size). For this, the animals were genotyped by PCR-RFLP (Avail) for FecB and the productive records of the herd analyzed. The allelic and genotypic frequencies were calculated, which, together with the non-genetic factors, were associated with litter size using a fixed-effect GLM model. Results. The FecBB allele presented lower frequency (0.379±0.152) than the FecB+ allele (0.622±0.152) for the whole OPC. These frequencies varied (p<0.05) between biotypes (Sudán: 0.486, Etíope: 0.271), the same occurred with the FecBBB genotype (0.078 in Etíope and 0.236 in Sudán). The FecB++ genotype was more frequent in Etíope (0.526) and the heterozygous genotype in Sudán (0.5) and for the OPC (0.448±0.070). No significant differences were found between biotypes for non-genetic factors. The prolificacy varied (p<0.05) between biotypes (1.45±0.22 in Etíope and 1.34±0.03 in Sudán), with an average of 1.40±0.11 for the OPC. None of the non-genetic factors, as well as the FecB genotypes, affected the litter size of the OPC (p>0.05). However, this was higher in the FecBBB genotype. Conclusions. The lucus studied was polymorphic. The litter size was not affected by non-genetic factors or the FecB genotype. These results can be used in assisted selection plans to increase OPC productivity.

Canine POMC deletion (P187fs) allele frequency in Labrador Retrievers in Brazil / Frequência de alelos mutados (P187fs) no POMC de cães Labrador Retriever no Brasil

The Labrador Retriever is among the main breeds with the greatest predisposition to obesity. Several factors, especially the interrelationships between food management, exercise and social factors; influence the likelihood of a dog becoming obese. Furthermore, genetic factors are also responsible for obesity in dogs, and in Labrador Retriever, a frameshift mutation (P187fs) in pro-opiomelanocortin (POMC) gene is strongly associated with obesity. There is no knowledge of studies that have previously evaluated the prevalence of the canine POMC deletion (P187fs) in Brazilian Labrador Retriever. Therefore, the objective of this study was to investigate this mutation in Labrador Retriever dogs in Brazil. Of the 108 Labrador Retrievers that were assessed in this study, 59 were from a previous study, composed by animals assisted in a veterinary hospital with unknown lineage, and 49 were from a prospective study, composed of 19 pet and 30 assistance/rescue Labrador Retriever dogs. The obesity risk and appetite questionnaire were applied, with some modifications, to tutors of the animals used in the prospective study. Fragments of the DNA, containing the mutation, were amplified by PCR and submitted to direct gene sequencing. The allele frequency of the mutation was 21.3% and was out of Hardy-Weinberg equilibrium (P<0.05). Using only the data of animals with known lineage, the presence of the mutated allele was higher in the Assistance/rescue Group than Pet Group (P<0.01), furthermore, the allele frequencies observed in Assistance Group (31.7%) was out of Hardy-Weinberg equilibrium (P<0.05), while that in the Pet Group (18.4%) was in equilibrium (P>0.05). Although the mutation has increased the food-motivation in the assistance/rescue dogs, other variables, especially frequent exercising, favored that these animals maintained the ideal body weight (body condition score = 5). In summary, the Hardy-Weinberg disequilibrium observed in the allele distribution of the deletion POMC_P187fs in this study, independently of the Labrador Retriever group assessed, suggesting the possibility of positive selection of the mutated allele, which may lead to the maintenance of this deleterious allele in the studied population.(AU)

O Labrador Retriever é uma das principais raças caninas com maior predisposição à obesidade. Vários fatores, especialmente as interrelações entre a alimentação, exercício e fatores sociais, influenciam a probabilidade de um cão se tornar obeso. Além disso, fatores genéticos são também responsáveis pela obesidade em cães, e no Labrador Retriever a mutação "frameshift" P187fs no gene pró-opiomelanocortina (POMC) está fortemente associada à obesidade. Não existem estudos prévios de prevalência da deleção P187fs no gene POMC em cães Labrador Retriever no Brasil. Portanto, o objetivo deste estudo foi investigar esta mutação em cães da raça Labrador Retriever no Brasil. Dos 108 Labradores Retrievers avaliados neste estudo, 59 eram de um estudo retrospectivo (composto por animais atendido no hospital veterinário e sem linhagem conhecida) e 49 eram de um estudo prospectivo (composto por 19 cães pet e 30 cães de assistência/resgate). Um questionário de risco de obesidade modificado foi aplicado nos tutores dos animais usados no estudo prospectivo. Fragmentos de DNA, contendo a mutação, foram amplificados por PCR e submetidos ao sequenciamento gênico direto. A frequência alélica da mutação foi de 21,3% e estava fora do equilíbrio de Hardy-Weinberg (P<0,05). Usando somente os dados dos animais de linhagem conhecida, a presença do alelo mutado foi maior no Grupo de cães de Assistência/resgate que no Grupo de Pets (P<0,01), além disso, as frequências alélicas nos Grupos de Assistência/resgate (31,7%) e no de pets (18,4%) estavam fora e em equilíbrio de Hardy-Weinberg (P<0,05), respectivamente. Embora a mutação tenha aumentado a motivação pelo alimento em cães Labrador Retriever do Grupo de Assistência/resgate, outras variáveis, especialmente o frequente exercício, favoreceu a manutenção o peso corporal ideal (peso corporal = 5). Em resumo, o desequilíbrio de Hardy-Weinberg observado na distribuição do alelo POMC_P187fs observado neste estudo, independentemente do grupo de Labrador Retriever avaliado, sugere a possibilidade de uma seleção positiva para o alelo mutado, o qual poderá levar a manutenção desse alelo deletério nesta população.(AU)

Polymorphisms of the calpain and calpastatin genes in two populations of colombian creole sheep / Polimorfismos de los genes calpaína y calpastatina en dos poblaciones de ovinos de pelo colombiano

ABSTRACT Objetive. Characterize the genetic polymorphism type SNPs in the calpain (CAPN) and calpastatin (CAST) genes of Colombian creole hair sheep (OPC). Materials and methods. In 300 individuals belonging to two OPC subpopulations from the departments of Sucre (SC) and Valle del Cauca (VC) were genotyped by PCR-RFLP (MspI) for the CAST locus and by PCR-SSCP for the CAPN locus. The allelic and genotypic frequencies, the observed (Ho) and expected heterozygosity (He), the fixation index (F) and the deviations from the Hardy-Weinberg equilibrium (HWE) were calculated and a molecular analysis of variance to estimate the values of FST, FIS and FIT. Results. In the CAST locus, the MM genotype was the most frequent (83.9±1.1%), followed by the other genotypes (MN: 15.5±1.1, NN: 6.0±0.0%) and the allelic frequency of M (91.7±0.4%) exceeded that of N (8.3±0.4%). For the CAPN locus the heterozygous genotype (48.2±0.7%) was the most frequent, the other genotypes presented frequencies TT:44.7 ± 1.9 and CC:7.0 ± 1.4%. The T allele reached a frequency of 68.8±1.5% (C: 31.3±1.5%). Similar percentages of allelic and genotypic frequencies were found in the subpopulations. The He was less than the Ho in both loci, with negative values of F and deviations of EHW only in CAPN. All the variation found was due to differences within the individuals, with non-significant values (p>0.05) of FST, FIS, and FIT (0.002, -0.093 and -0.095, respectively). Conclusions. The loci studied has high variability, these results can be used for future gene-assisted selection plans to increase OPC productivity.

RESUMEN Objetivo. El propósito del presente estudio fue caracterizar el polimorfismo genético tipo SNPs en los genes calpaína (CAPN) y calpastatina (CAST) en el ovino de pelo criollo colombiano (OPC). Materiales y métodos. 300 individuos pertenecientes a dos subpoblaciones de OPC de los departamentos de Sucre (SC) y Valle del Cauca (VC) fueron genotipados por PCR-RFLP (MspI) para el locus CAST y por PCR-SSCP para el locus CAPN. Se calcularon las frecuencias genotípicas, alélicas, la heterocigocidad observada (Ho) y esperada (He), el índice de fijación (F), los desvíos del equilibrio de Hardy-Weinberg (EHW) y un análisis de varianza molecular para estimar los valores de FST, FIS y FIT. Resultados. En el locus CAST, el genotipo MM fue el más frecuente (83.9±1.1%), seguido por los otros genotipos (MN: 15.5±1.1; NN:6.0±0.0%) y la frecuencia alélica de M (91.7±0.4%) superó la del N (8.3±0.4%). Para el locus CAPN el genotipo heterocigoto (48.2±0.7%) fue el más frecuente; los otros genotipos presentaron frecuencias de TT:44.7±1.9 y CC:7.0±1.4%. El alelo T alcanzó una frecuencia de 68.8±1.5% (C:31.3±1.5%). Similares frecuencias alélicas y genotípicas se encontraron en las subpoblaciones. La He fue menor que la Ho en ambos loci, con valores negativos de F y desvíos de EHW solo en CAPN. Toda la variación encontrada fue debida a diferencias dentro de los individuos, con valores no significativos (p>0.05) de FST, FIS y FIT (0.002, -0.093 y -0.095, respectivamente). Conclusiones. Los loci estudiados tiene alta variabilidad, estos resultados pueden ser utilizados para futuros planes de selección asistida por genes para aumentar la productividad del OPC.

Enrichment of rare alleles within epigenetic chromatin marks in the first intron

In previous studies, we demonstrated that some sites in the first intron likely regulate gene expression. In the present work, we sought to further confirm the functional relevance of first intron sites by estimating the quantity of rare alleles in the first intron. A basic hypothesis posited herein is that genomic regions carrying more functionally important sites will have a higher proportion of rare alleles. We estimated the proportions of rare single nucleotide polymorphisms with a minor allele frequency < 0.01 located in several histone marks in the first introns of various genes, and compared them with those in other introns and those in 2-kb upstream regions. As expected, rare alleles were found to be significantly enriched in most of the regulatory sites located in the first introns. Meanwhile, transcription factor binding sites were significantly more enriched in the 2-kb upstream regions (i.e., the regions of putative promoters of genes) than in the first introns. These results strongly support our proposal that the first intron sites of genes may have important regulatory functions in gene expression independent of promoters.

Polymorphism and Forensic Application Value of 71 Y-SNP Loci in Han Population of Northwest China / 法医学杂志

OBJECTIVES@#To analyze the polymorphism of 71 SNP loci on Y chromosome in Han population of Northwest China, to assess its forensic application value, and to screen out Y-SNP loci for forensic examination of Han population in East, South, and Northwest China based on the integration of previous research results.@*METHODS@#Multiplex polymerase chain reaction （PCR） and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-TOF-MS） were performed on 71 Y-SNP loci of 202 unrelated Han male individuals in Northwest China. Gene diversity （GD） and haplotype diversity （HD） values were calculated, and then Y-SNP loci of Han population in East, South, and Northwest China were screened with the combination of data from previous research.@*RESULTS@#Among the detected 71 loci, 67 loci were polymorphic in the Northwest Han male population, with GD values 0.010 0-0.502 2. There were 22 and 25 loci with a moderate （0.2≤GD<0.3） and high （GD≥0.3） amount of genetic information, respectively. There were 26 loci for the Han communities in Northwest, South, and East China.@*CONCLUSIONS@#Y-SNP loci are potential in paternity testing and individual identification, as well as the judgement of population distribution and migration.

VEGF-A and ARMS2 gene polymorphism on AMD susceptibility / Шинэ санаа Шинэ нээлт

Background@#Age-related macular degeneration (AMD) is an eye condition, that occurs people aged above 50, leads to gradual loss of the vision because of a damage in the macula, which is located in the center of the retina. Several polymorphisms in different genes have been proposed as factors that increase the disease susceptibility. Therefore, we investigated the association between rs833061 polymorphism of VEGF-A gene and rs10490924 polymorphism of ARMS2 gene and AMD in order to analyze with other similar studies by meta analysis.@*Purpose@#To investigate the polymorphisms of VEGF-A gene and ARMS2 gene on AMD susceptibility@*Methods@#is case-control study was conducted on 74 AMD patients and 32 unaffected age-and gender-matched control individuals. Genomic DNA was extracted from the peripheral venous blood. The single nucleotide polymorphisms were identified by restriction fragment length polymorphism (RFLP) method and results confirmed by gel electrophoresis. The REVIEW MANAGER 5.2 software and MetaXL was used for meta-analysis@*Results@#We did not find statistically significant differences in С allele and СС genotype frequency of rs833061 polymorphism of VEGF-A gene between patients and controls. However, analysis of rs10490924 polymorphism of ARMS2 gene shows that T allele (OR=2.72, 95% CI, 1.47 – 5.02, p=0.001), TT genotype (OR=4.54, 95% CI, 1.49 – 13.87,p=0.019) were significantly associated with AMD risk. Haplotype analysis of these SNPs showed that C+T haplotype was statistically significantly different (OR=5.23, 95% CI, 1.76-15.54, p=0.002) between patients and controls.@*Conclusion@#As shown by results, rs10490924 polymorphism of ARMS2 gene show that T allele, TT genotype and C+T haplotype were significantly associated with AMD risk In meta-analysis, T allele of rs10490924 polymorphism of ARMS2 gene was significantly associated with AMD risk in all ethnicity that include Asian and Caucasian. However, T allele prevalence was higher in Asians.

MTHFR C677T and A1298C Gene Polymorphisms and Ischemic Heart Disease (IHD) in a Sri Lankan Population - A Preliminary Study

MTHFR A1298C and C677T SNPs are now recognised as important genetic mutations which would give rise to hyperhomocysteinemia. In this study, we analysed the prevalence of these two SNPs in 79 ischemic heart disease (IHD) patients awaiting coronary artery bypass grafting and 79 healthy subjects. MHFR polymorphisms were analysed using polymerase chain reaction followed by a restriction fragment analysis. Prevalence rates for MTHFR C677T polymorphism were 72.8%, 24.7%, and 2.5% for CC, CT, and TT genotypes, respectively, for the whole study population with 677CC genotype being the predominant genotype among both the IHD patients and the controls. The 677TT genotype was detected only among the IHD patients. There was no significant difference in MTHFR 677 genotype variations between IHD patients and the control group. Prevalence rates for the MTHFR A1298C polymorphism were 50%, 37.3%, and 12.7% for the AA, AC, and CC genotypes, respectively, for the whole study population with 1298AA genotype being the predominant genotype among controls and 1298AC the predominant genotype among IHD patients. There was a significant difference (p < 0.01) between IHD patients and controls when the MTHFR 1298 genotype variations were compared. Allele frequencies for the mutant T allele for C677T mutation at 0.149 are the highest reported from Sri Lanka. The frequency of the C for the A1298C mutation was 0.313. Results of this study indicate that MTHFR A1298C SNP is more prevalent in Sri Lankans when compared to C677T SNP and that the mutant forms of the MTHFR A1298C SNP are associated with ischemic heart disease.

Association of CDKAL1, CDKN2A/B & HHEX gene polymorphisms with type 2 diabetes mellitus in the population of Hyderabad, India.

Background & objectives: The genome-wide association studies (GWAS) have shown an association of type 2 diabetes mellitus (T2DM) with several novel genes. We report here the findings on the pattern of genetic association of three genes (CDKAL1, CDKN2A/B and HHEX) with T2DM in the population of Hyderabad, south India. Methods: A sample of 1379 individuals (758 T2DM cases and 621 controls) from Hyderabad, India, were genotyped for five single nucleotide polymorphisms (SNPs) of CDKAL1 (rs7754840, rs7756992) CDKN2A/B (rs10811661) and HHEX (rs1111875, rs7923837) genes on Sequenom Mass Array platform. Results: The risk allele frequencies of the CDKAL1 and CDKN2A/B SNPs were relatively higher in cases than in the controls and the logistic regression analysis yielded significant odds ratios suggesting that the variant alleles conferred risk for developing T2DM in this population. The HHEX gene did not show either allelic or genotypic association with T2DM. The multivariate logistic regression analysis with reference to both alleles and genotypes of CDKAL1 SNPs showed significant association, suggesting an important role for this gene in the T2DM pathophysiology. Interpretation & conclusions: A significant association was seen of all the three SNPs of CDKAL1 and CDKN2A/B genes with T2DM but none of the two SNPs of HHEX. Further studies are required to cross-validate our findings in a relatively larger sample. It is also necessary to explore other SNPs of HHEX gene to unequivocally establish the pattern of association of this gene with T2DM in this population.

Genetic diversity through human leukocyte antigen typing in end‑stage renal disease patients and prospective donors of North India.

As the incidence of end-stage renal disease (ESRD) is rapidly increasing, the demand for dialysis and transplantation has dramatically increased, which has led to concerns about the availability and equitable allocation of kidneys for transplantation. The distribution of HLA-A, B and DR alleles in 148 renal transplant recipients and 191 live related prospective donors from 2009 to 2010 were analyzed. Allele frequencies and haplotype frequencies were calculated in recipients and donors. The prospective donors were further analyzed on the basis of their relationship to the patients and according to the sex ratio. A significant female preponderance was noted in the prospective donor population, most of whom were either siblings or parents of the recipients. On the contrary, the recipient population predominantly comprised of males. The most frequent HLA-A, HLA-B, HLA-DRB1 alleles in renal transplant patients were HLA-A*11, A*02, A*01, A*24; HLA-B*35, B*40, B*44, B*15, B*52, and HLA-DRB1*15, DRB1*07, DRB1*13, DRB1*11 respectively. The most frequent HLA-A, HLA-B, HLA-DRB1 alleles in prospective donors were HLA-A*02, A*11, A*33, A*24; HLA-B*35, B*44, B*40, B*15 and HLA-DRB1*15, DRB1*07, DRB1*11, DRB1*13 respectively. A*11-B*35, A*02-DRB1*15, B*40- DRB1*15 were the most common HLA A-B , HLA A-DR, HLA B-DR haplotypes respectively in renal transplant patients, whereas, A*11-B*35, A*11-DRB1*15, B*44-DRB1*07 were the most common haplotypes in renal donors. In three locus haplotype, HLA-A*02-B*40-DRB1*15 was the most frequent haplotype in patients, whereas, in prospective renal donors HLA-A*33-B*44-DRB1*07 was the most frequent haplotype.

Analysis on characteristics of fifteen short tandem repeat genetic polymorphisms in Yunnan Han population / 中国免疫学杂志

Objective:To research on the genetic polymorphism distributions of fifteen short tandem repeat ( STR ) loci (D8S1179,D21S11,D7S820,CSF1PO,D3S1358,TH01,D13S317,D16S539,D2S1338,D19S433,VWA,TPOX,D18S51,D5S818, FGA) in Han race of Yunnan. Methods:A total of 313 specimens were collected from the unrelated individuals in Yunnan Han popu-lation. Genome DNA was extracted and amplified by multiplex PCR technique,the PCR products were analyzed by ABI-3130 genetic analyzer capillary electrophoresis detection, collected statistics of each STR loci genotypic frequency, and carried out the Hardy-Weinberg Genetic balance test. Results: No significant deviation from the Hardy-Weinberg Equilibrium was observed ( P>0. 05 ) , the heterozygosity of the fifteen STR loci in Yunnan Han population were found to be 0. 636-0. 901, Probability match was 0. 034-0. 220. Discrimination power of signal STR loci was 0. 780-0. 966, power of paternity exclusion was 0. 336-0. 797, polymorphism information content was 0. 555-0. 860,the combined accumulation discrimination power and exclusion probability for the 15 STR loci in Yunnan Han population were determined to be more than 0. 999 999 99 and 0. 999 998 408. The allele frequency of the 15 STR loci had a similarity compared with other areas in China,but also had a slight regional differences. Conclusion: The 15 STR loci( D8S1179, D21S11,D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA ) demonstrate high genetic polymorphism in Yunnan Han population, they have a high forensic science application value in paternity testing and individual identification.

Population genetic study of 10 short tandem repeat loci from 600 domestic dogs in Korea

Dogs have long shared close relationships with many humans. Due to the large number of dogs in human populations, they are often involved in crimes. Occasionally, canine biological evidence such as saliva, bloodstains and hairs can be found at crime scenes. Accordingly, canine DNA can be used as forensic evidence. The use of short tandem repeat (STR) loci from biological evidence is valuable for forensic investigations. In Korea, canine STR profiling-related crimes are being successfully analyzed, leading to diverse crimes such as animal cruelty, dog-attacks, murder, robbery, and missing and abandoned dogs being solved. However, the probability of random DNA profile matches cannot be analyzed because of a lack of canine STR data. Therefore, in this study, 10 STR loci were analyzed in 600 dogs in Korea (344 dogs belonging to 30 different purebreds and 256 crossbred dogs) to estimate canine forensic genetic parameters. Among purebred dogs, a separate statistical analysis was conducted for five major subgroups, 97 Maltese, 47 Poodles, 31 Shih Tzus, 32 Yorkshire Terriers, and 25 Pomeranians. Allele frequencies, expected (Hexp) and observed heterozygosity (Hobs), fixation index (F), probability of identity (P(ID)), probability of sibling identity (P(ID)(sib)) and probability of exclusion (PE) were then calculated. The Hexp values ranged from 0.901 (PEZ12) to 0.634 (FHC2079), while the P(ID)(sib) values were between 0.481 (FHC2079) and 0.304 (PEZ12) and the P(ID)(sib) was about 3.35 × 10⁻⁵ for the combination of all 10 loci. The results presented herein will strengthen the value of canine DNA to solving dog-related crimes.

Clinical Heterogeneity of Atypical Pantothenate Kinase-Associated Neurodegeneration in Koreans

OBJECTIVE: Neurodegeneration with brain iron accumulation (NBIA) represents a group of inherited movement disorders characterized by iron accumulation in the basal ganglia. Recent advances have included the identification of new causative genes and highlighted the wide phenotypic variation between and within the specific NBIA subtypes. This study aimed to investigate the current status of NBIA in Korea. METHODS: We collected genetically confirmed NBIA patients from twelve nationwide referral hospitals and from a review of the literature. We conducted a study to describe the phenotypic and genotypic characteristics of Korean adults with atypical pantothenate kinase-associated neurodegeneration (PKAN). RESULTS: Four subtypes of NBIA including PKAN (n = 30), PLA2G6-related neurodegeneration (n = 2), beta-propeller protein-associated neurodegeneration (n = 1), and aceruloplasminemia (n = 1) have been identified in the Korean population. The clinical features of fifteen adults with atypical PKAN included early focal limb dystonia, parkinsonism-predominant feature, oromandibular dystonia, and isolated freezing of gait (FOG). Patients with a higher age of onset tended to present with parkinsonism and FOG. The p.R440P and p.D378G mutations are two major mutations that represent approximately 50% of the mutated alleles. Although there were no specific genotype-phenotype correlations, most patients carrying the p.D378G mutation had a late-onset, atypical form of PKAN. CONCLUSIONS: We found considerable phenotypic heterogeneity in Korean adults with atypical PKAN. The age of onset may influence the presentation of extrapyramidal symptoms.

Frequency of Wra antigen and anti-Wra in Brazilian blood donors

BACKGROUND: Wra is a low-incidence antigen, which is antithetical to the high prevalence red blood cell antigen, Wrb. Anti-Wra is a naturally occurring antibody that is found in approximately 1-2% of blood donors. The aim of this study was to determine the frequency of Wra and anti-Wra in Brazilian blood donors.METHODS: A total of 1662 Brazilian blood donors were molecularly analyzed using the SNaPshot methodology to determine the WR*A/B alleles and to predict the frequency of the Wra antigen. To detect the anti-Wra, samples from 1049 blood donors were analyzed using a gel test with Wr(a+) red blood cells. The serum was treated with dithiothreitol (DTT) to determine the immunoglobulin classes. Immunoglobulin (Ig)-G isotype classification was performed in a gel test using the IgG1/IgG3 card. A monocyte monolayer assay was employed to predict the clinical significance of IgG anti-Wra.RESULTS: Of the 1662 donors, only one sample had the DI*02.03 allele in heterozygous predicting the Wr(a+b+) phenotype. Anti-Wra was detected in 34 (3.24%) samples, 64.7% in females and 35.3% in males. Regarding the immunoglobulin class, eight (23.5%) cases of anti-Wra were classified as IgG and 26 (76.5%) as IgM. Of the eight cases of IgG anti-Wra, four were IgG1, two were IgG3 and three anti-Wra were not IgG3 or IgG1, and thus probably IgG2 or IgG4. The results of the monocyte monolayer assay showed that IgG anti-Wra might be of clinical significance.CONCLUSION: This study shows a very low frequency (0.06%) of the Wra antigen in Brazilian blood donors. Additionally, it shows that the frequency of anti-Wra in this population is higher than previously reported.

Análise de frequências alélicas de 15 marcadores STR em alunos da Faculdade de Odontologia de Bauru / Allelic frequency analysis of 15 STR markers in students from Bauru School of Dentistry

Entre as muitas aplicações das tecnologias de identificação biológica humana, estão as finalidades forenses. O objetivo desta pesquisa foi verificar frequências alélicas de Short Tandem Repeat (STR) e os parâmetros estatísticos de interesse em genética de populações e forense para desenvolver o primeiro banco de dados populacional de DNA na Faculdade de Odontologia de Bauru, Universidade de São Paulo, (FOB/USP) para futuros usos forenses. Frequências alélicas de 15 locos autossômicos e do marcador de gênero amelogenina foram determinadas utilizando amostras de 200 μL de saliva doados por 296 alunos de graduação da FOB/USP, com idade ≥ 18 anos, após aprovação ética. Os testes laboratoriais foram feitos com kits comerciais. Resultados e parâmetros estatísticos foram obtidos por meio de programas clássicos: GeneMapper-ID-X, MS Excel 2002 versão 10.6871.6870, GenAlEx 6.5 e Arlequin 3.5, comparando quatro populações (brasileira, portuguesa, norte-americana e a população deste estudo). Os locos mais polimórficos foram D18S51 (17 alelos) e FGA (15 alelos), seguidos pelo D21S11 (13 alelos) e os menos polimórficos foram D16S539 e TH01 (7 alelos cada). A análise comparativa com amostra da população brasileira proveniente de estudos anteriores (n > 100.000) pelo teste goodness of fit X2 index não mostrou diferenças significativas entre estes grupos (p = 0,9999). Outros parâmetros estatísticos foram calculados comparando as populações: local (deste estudo), portuguesa e norte-americana. A análise de variância molecular (AMOVA) entre as três populações, entre as pessoas da mesma população e para cada pessoa de cada população mostrou que existe uma elevada variância individual (99%), que esta variância é mantida uniformemente entre as pessoas da mesma amostra/região (1%) e entre as três populações estudadas (0%). O estudo confirmou o elevado grau de polimorfismo e a alta heterozigosidade (96,5%) da população. Houve diferença significativa quanto ao gênero (79,7% mulheres)...

There are many ways of applying biological human identification technologies, among these are forensic applications. The objective of this study was to verify allele frequencies for 15 autosomal short tandem repeat (STR) loci and develop the first human DNA population database at the Bauru School of Dentistry, University of São Paulo (FOB/USP), for future forensic uses. Allele frequencies for these STR loci and an amelogenin gender marker were determined using 200 μL samples of saliva donated by 296 undergraduates from FOB/USP who were ≥ 18 years old at the time of the sample collect after signing a consent form with ethical approval. For laboratory tests, commercial kits were used. Results and statistical parameters were obtained using the following software: GeneMapper IDX (version 1.5), MS Excel 2002 (version 10.6871.6870), GenAlEx (version 6.5) and Arlequin (version 3.5) to compare four populations (Brazil, Portugal, U.S. and this study population). Results indicated that the most polymorphic loci were D18S51 (17 alleles) and FGA (15 alleles), followed by D21S11 (13 alleles); the least polymorphic loci were D16S539 and TH01 (7 alleles each). Various Brazilian populations (n > 100,000) from other studies were compared with this studys Brazilian population using a goodness-of-fit chi-squared test, and no significant differences in these frequencies were observed between these two population groups (p = 0.9999). Other forensic and population genetic statistical parameters were calculated comparing this studys population with Portugal and U.S. populations. For example, an analysis of molecular variance (AMOVA) among all populations, among people of the same population and for each person for each population, showed that people have high individual variance (99%) and that this variance is maintained evenly between people of the same sample/region (1%) and among the three populations studied (0%). This study reinforced the conclusion of other allele frequency...

Análise de frequências alélicas de 15 marcadores STR em alunos da Faculdade de Odontologia de Bauru / Allelic frequency analysis of 15 STR markers in students from Bauru School of Dentistry

Entre as muitas aplicações das tecnologias de identificação biológica humana, estão as finalidades forenses. O objetivo desta pesquisa foi verificar frequências alélicas de Short Tandem Repeat (STR) e os parâmetros estatísticos de interesse em genética de populações e forense para desenvolver o primeiro banco de dados populacional de DNA na Faculdade de Odontologia de Bauru, Universidade de São Paulo, (FOB/USP) para futuros usos forenses. Frequências alélicas de 15 locos autossômicos e do marcador de gênero amelogenina foram determinadas utilizando amostras de 200 μL de saliva doados por 296 alunos de graduação da FOB/USP, com idade ≥ 18 anos, após aprovação ética. Os testes laboratoriais foram feitos com kits comerciais. Resultados e parâmetros estatísticos foram obtidos por meio de programas clássicos: GeneMapper-ID-X, MS Excel 2002 versão 10.6871.6870, GenAlEx 6.5 e Arlequin 3.5, comparando quatro populações (brasileira, portuguesa, norte-americana e a população deste estudo). Os locos mais polimórficos foram D18S51 (17 alelos) e FGA (15 alelos), seguidos pelo D21S11 (13 alelos) e os menos polimórficos foram D16S539 e TH01 (7 alelos cada). A análise comparativa com amostra da população brasileira proveniente de estudos anteriores (n > 100.000) pelo teste goodness of fit X2 index não mostrou diferenças significativas entre estes grupos (p = 0,9999). Outros parâmetros estatísticos foram calculados comparando as populações: local (deste estudo), portuguesa e norte-americana. A análise de variância molecular (AMOVA) entre as três populações, entre as pessoas da mesma população e para cada pessoa de cada população mostrou que existe uma elevada variância individual (99%), que esta variância é mantida uniformemente entre as pessoas da mesma amostra/região (1%) e entre as três populações estudadas (0%). O estudo confirmou o elevado grau de polimorfismo e a alta heterozigosidade (96,5%) da população. Houve diferença significativa quanto ao gênero (79,7% mulheres)...

There are many ways of applying biological human identification technologies, among these are forensic applications. The objective of this study was to verify allele frequencies for 15 autosomal short tandem repeat (STR) loci and develop the first human DNA population database at the Bauru School of Dentistry, University of São Paulo (FOB/USP), for future forensic uses. Allele frequencies for these STR loci and an amelogenin gender marker were determined using 200 μL samples of saliva donated by 296 undergraduates from FOB/USP who were ≥ 18 years old at the time of the sample collect after signing a consent form with ethical approval. For laboratory tests, commercial kits were used. Results and statistical parameters were obtained using the following software: GeneMapper IDX (version 1.5), MS Excel 2002 (version 10.6871.6870), GenAlEx (version 6.5) and Arlequin (version 3.5) to compare four populations (Brazil, Portugal, U.S. and this study population). Results indicated that the most polymorphic loci were D18S51 (17 alleles) and FGA (15 alleles), followed by D21S11 (13 alleles); the least polymorphic loci were D16S539 and TH01 (7 alleles each). Various Brazilian populations (n > 100,000) from other studies were compared with this studys Brazilian population using a goodness-of-fit chi-squared test, and no significant differences in these frequencies were observed between these two population groups (p = 0.9999). Other forensic and population genetic statistical parameters were calculated comparing this studys population with Portugal and U.S. populations. For example, an analysis of molecular variance (AMOVA) among all populations, among people of the same population and for each person for each population, showed that people have high individual variance (99%) and that this variance is maintained evenly between people of the same sample/region (1%) and among the three populations studied (0%). This study reinforced the conclusion of other allele frequency...

SNPs analysis of ABCA4 gene in Han Chinese in Beijing / 实用口腔医学杂志

Objective:To provide the basis of single nucleotide polymorphism(SNPs)for identification and analysis of ABCA4 gene related etiologic studies in Han Chinese in Beijing(CHB).Methods:SNPs of ABCA4 gene were analyzed for minor allele frequencies (MAFs),haplotype frequencies,linkage disequilibrium patterns,and tag SNPs by Haploview program using the HapMap data.Re-sults:129(37.6%)of 343 SNPs were monotonic.95 tagging SNPs were identified in 214 eligible SNPs with 3 haplotype blocks identi-fied.The frequencies of the top 2 haplotypes among each of the 3 haplotype blocks were between 91.1% and 94.0%.Conclusion:SNPs in ABCA4 gene were analyzed by Haploview program.The analysis provides clues for future studies involving this gene.