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The pleiotropic nature of the apolipoprotein E (APOE) gene is associated with complex diseases in different populations. We analyzed APOE polymorphisms in 76 individuals from Jujuy - Argentina using NGS technology. The observed genotypes align with the expected Hardy-Weinberg equilibrium. APOE3 was the most common allele, followed by APOE4 and APOE2. The allele distribution pattern is consistent with findings in previously studied populations of Native Americans and Asians. The E4 allele's low frequency, always observed in a heterozygous state, raises questions regarding its relevance in explaining dementia and longevity associated with this marker in the Central Andes.

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Short tandem repeat (STR) markers on the X chromosome have a high potential for solving complex kinship analysis and individual identification cases. To achieve such purposes, allele and haplotype frequencies for the specific population are necessary. Nonetheless, such frequencies are not always available. Therefore, we obtained haplotypes from 520 unrelated males from four different geographic regions of Espírito Santo - Brazil, using the Investigator Argus X-12 kit. Forensic parameters for linked groups of four X-STR loci are reported. Genetic distance analyzes suggest that ES population is genetically closer to the Italian population and farther from the Mexican one, among the populations analyzed in this study.

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Gaucher disease (GD) is an autosomal recessive lysosomal disorder caused by pathogenic variants in GBA1 which result in the deficient activity of glucocerebrosidase (GCase). There are few data on the genetic characterization of Brazilian GD patients. This study aimed at characterizing the genotype of 72 unrelated Brazilian GD patients (type I = 63, type II = 4, type III = 5; male = 31). Forty patients were from South Brazil (SB), and 32 were from other regions of Brazil (Others). The exons and exon/intron junctions of GBA1 were analyzed by Sanger sequencing in 8 patients, or by massive parallel sequencing followed by Sanger of exons 9 and 10 in 64 patients. In total, 31 pathogenic variants were identified. The most frequent allele found was N370S (p.(Asn409Ser)) (41.0%), and the most frequent genotype was N370S/RecNciI p.[Asn409Ser];[Leu483Pro;Ala495Pro;Val499=](23.6%). Three variants (N370S - in exon 9, and RecNciI and L444P (p.(Leu483Pro), in exon 10) correspond to 76.3% of total alleles in SB and 59.4% in Others. Two novel variants were described: c.326del(p.(Gln109Argfs*9)) and c.690G>A (p.(?)). Although sequencing all the exons of GBA1 is the gold-standard method for the genetic analysis of GD patients, a step analysis can be proposed for Brazilian patients, starting with analysis of exons 9 and 10. The N370S allele is the most frequently associated with GD in Brazil.

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JAK2V617F (dbSNP: rs77375493) is the most frequent and most-studied variant in BCR::ABL1 negative myeloproliferative neoplasms and in the JAK2 gene. The present study aimed to molecularly characterize variants in the complete coding region of the JAK2 gene in patients with BCR::ABL1 negative chronic myeloproliferative neoplasms. The study included 97 patients with BCR::ABL1 negative myeloproliferative neoplasms, including polycythemia vera (n=38), essential thrombocythemia (n=55), and myelofibrosis (n=04). Molecular evaluation was performed using conventional PCR and Sanger sequencing to detect variants in the complete coding region of the JAK2 gene. The presence of missense variants in the JAK2 gene including rs907414891, rs2230723, rs77375493 (JAK2V617F), and rs41316003 were identified. The coexistence of variants was detected in polycythemia vera and essential thrombocythemia. Thus, individuals with high JAK2V617F variant allele frequency (≥50% VAF) presented more thrombo-hemorrhagic events and manifestations of splenomegaly compared with those with low JAK2V617F variant allele frequency (<50% VAF). In conclusion, individuals with BCR::ABL1 negative neoplasms can display >1 variant in the JAK2 gene, especially rs2230722, rs2230724, and rs77375493 variants, and those with high JAK2V617F VAF show alterations in the clinical-laboratory profile compared with those with low JAK2V617F VAF.

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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.

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BACKGROUND: Brazil is the largest grower of the world's 26 million ha of sugarcane, Saccharum officinarum. Pest damage mainly by the sugarcane borer, Diatraea saccharalis (F.), is a great challenge to the sugarcane industry. To control D. saccharalis, Brazil launched the world's first commercial use of Bt sugarcane in 2017. As part of the resistance management programs for Bt sugarcane planting, 535 F2 isoline families of D. saccharalis collected from three major sugarcane planting states (Goiás, Minas Gerais and São Paulo) in Brazil during 2019-2020 were screened for resistance to two Bt sugarcane varieties: CTC20BT expressing Cry1Ab and CTC9001BT expressing Cry1Ac. Here we report the results of the first study related to Bt resistance in a sugarcane cropping system. RESULTS: Larval survivorships of these families in an F2 screen on CTC20BT were highly correlated with their survival on CTC9001BT, whereas the Cry1Ac tissues exhibited greater insecticidal activities than Cry1Ab. Resistance allele frequencies (RAFs) for populations from Goiás and Minas Gerais were relatively low at 0.0034 for Cry1Ab and 0.0045 to Cry1Ac. By contrast, RAFs for São Paulo populations were considerably greater (0.0393 to Cry1Ab, 0.0245 to Cry1Ac). CONCLUSIONS: RAFs to Cry1Ab and Cry1Ac varied among Brazilian D. saccharalis populations. Prior selection resulting from an intensive use of single-gene Bt maize under low compliance of refuge planting could be a main factor contributing to the high RAF in São Paulo. The results suggest that mitigation measures including sufficient non-Bt maize refuge planting, effective resistance monitoring, and use of pyramided Bt sugarcane traits should be implemented promptly to prevent further increase in the RAF to ensure the sustainable use of Bt sugarcane in Brazil. MINI ABSTRACT: To control Diatraea saccharalis, Brazil launched the world's first commercial use of Bt sugarcane in 2017. As part of the resistance management programs for Bt sugarcane planting in Brazil, 535 F2 isoline families of D. saccharalis collected from three major sugarcane planting states (Goiás, Minas Gerais and São Paulo) in Brazil during 2019-2020 were screened for resistance to Cry1Ab and Cry1Ac sugarcane plants Resistance allele frequencies (RAFs) for the populations from Goiás and Minas Gerais were relatively low at 0.0034 for Cry1Ab and 0.0045 to Cry1Ac. By contrast, RAFs for the São Paulo populations were considerably greater (0.0393 to Cry1Ab, 0.0245 to Cry1Ac). Prior selection resulting from an intensive use of single-gene Bt maize under low compliance of non-Bt maize refuge planting could be a main factor contributing to the high RAF in São Paulo. The results suggest that effective mitigation measures including sufficient non-Bt maize refuge planting, effective resistance monitoring and use of pyramided Bt sugarcane traits should be implemented promptly to prevent further increase in the RAF to ensure the sustainable use of Bt sugarcane in Brazil. © 2022 Society of Chemical Industry.

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Trypanosoma cruzi the causative agent of Chagas disease shows a marked genetic diversity and divided into at least six Discrete Typing Units (DTUs). High intra genetic variability has been observed in the TcI DTU, the most widely distributed DTU, where patterns of genomic diversity can provide information on ecological and evolutionary processes driving parasite population structure and genome organization. Chromosomal aneuploidies and rearrangements across multigene families represent an evidence of T. cruzi genome plasticity. We explored genomic diversity among 18 Colombian T. cruzi I clones and 15 T. cruzi I South American strains. Our results confirm high genomic variability, heterozygosity and presence of a clade compatible with the TcIdom genotype, described for strains from humans in Colombia and Venezuela. TcI showed high structural plasticity across the geographical region studied. Differential events of whole and segmental aneuploidy (SA) along chromosomes even between clones from the same strain were found and corroborated by the depth and allelic frequency. We detected loss of heterozygosity (LOH) events in different chromosomes, however, the size and location of segments under LOH varied between clones. Genes adjacent to breakpoints were evaluated, and retrotransposon hot spot genes flanked the beginning of segmental aneuploidies. Our results suggest that T. cruzi genomes, like those of Leishmania, may have a highly unstable structure and there is now an urgent need to design experiments to explore any potential adaptive role for the plasticity observed.

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Genetic and omics analyses frequently require independent observations, which is not guaranteed in real datasets. When relatedness cannot be accounted for, solutions involve removing related individuals (or observations) and, consequently, a reduction of available data. We developed a network-based relatedness-pruning method that minimizes dataset reduction while removing unwanted relationships in a dataset. It uses node degree centrality metric to identify highly connected nodes (or individuals) and implements heuristics that approximate the minimal reduction of a dataset to allow its application to complex datasets. When compared with two other popular population genetics methodologies (PLINK and KING), NAToRA shows the best combination of removing all relatives while keeping the largest possible number of individuals in all datasets tested and also, with similar effects on the allele frequency spectrum and Principal Component Analysis than PLINK and KING. NAToRA is freely available, both as a standalone tool that can be easily incorporated as part of a pipeline, and as a graphical web tool that allows visualization of the relatedness networks. NAToRA also accepts a variety of relationship metrics as input, which facilitates its use. We also release a genealogies simulator software used for different tests performed in this study.

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This study aimed to investigate the prediction ability for growth and maternal traits using different low-density customized SNP arrays selected by informativeness and distribution of markers across the genome employing single-step genomic BLUP (ssGBLUP). Phenotypic records for adjusted weight at 210 and 450 days of age were utilized. A total of 945 animals were genotyped with high-density chip, and 267 individuals born after 2008 were selected as validation population. We evaluated 11 scenarios using five customized density arrays (40 k, 20 k, 10 k, 5 k and 2 k) and the HD array was used as desirable scenario. The GEBV predictions and BIF (Beef Improvement Federation) accuracy were obtained with BLUPF90 family programs. Linear regression was used to evaluate the prediction ability, inflation, and bias of GEBV of each customized array. An overestimation of partial GEBVs in contrast with complete GEBVs and increase of BIF accuracy with the density arrays diminished were observed. For all traits, the prediction ability was higher as the array density increased and it was similar with customized arrays higher than 10 k SNPs. Level of inflation was lower as the density array increased of and was higher for MW210 effect. The bias was susceptible to overestimation of GEBVs when the density customized arrays decreased. These results revealed that the BIF accuracy is sensible to overestimation using low-density customized arrays while the prediction ability with least 10,000 informative SNPs obtained from the Illumina BovineHD BeadChip shows accurate and less biased predictions. Low-density customized arrays under ssGBLUP method could be feasible and cost-effective in genomic selection.

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The HLA compatibility continues to be the main limitation when finding compatible donors, especially if an identical match is not found within the patient's family group. The creation of bone marrow registries allowed a therapeutic option by identifying 10/10 compatible unrelated donors (URD). However, the availability and frequency of haplotypes and HLA alleles are different among ethnic groups and geographical areas, increasing the difficulty of finding identical matches in international registries. In this study, the HLA-A, -B, -C, -DRB1, and -DQB1 loci of 1763 donors registered in the Colombian Bone Marrow Registry were typed by next-generation sequencing. A total of 52 HLA-A, 111 HLA-B, 41 HLA-C, 47 HLA-DRB1, and 20 HLA-DQB1 alleles were identified. The 3 most frequent alleles for each loci were A*24:02g (20,8%), A*02:01g (16,1%), A*01:01g (7.06%); B*35:43g (7.69%), B*40:02g (7.18%), B*44:03g (6.07%); C*04:01g (15.40%), C*01:02g (10.49%), C*07:02g (10.44%); DRB1*04:07g (11.03%), DRB1*07:01g (9.78%), DRB1*08:02g (6.72%); DQB1*03:02g (20.96%), DQB1*03:01g (17.78%) and DQB1*02:01g (16.05%). A total of 497 HLA-A-C-B-DRB1-DQB1 haplotypes were observed with a frequency greater than or equal to 0.05% (> 0.05%); the haplotypes with the highest frequency were A*24:02g~B*35:43g~C*01:02g~DQB1*03:02g~DRB1*04:07g (3.34%), A*29:02g~B*44:03g~C*16:01g~DQB1*02:01g~DRB1*07:01g (2.04%), and A*01:01g~B*08:01g~C*07:01g~DQB1*02:01g~DRB1*03:01g (1.83%). This data will allow the new Colombian Bone Marrow Donor Registry to assess the genetic heterogeneity of the Colombian population and serve as a tool of interest for future searches of unrelated donors in the country.

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