Unique DNA Fingerprints Research Articles

Species Identification of Sea Bamboo (Isis hippuris) using COI-based DNA Barcoding

Conservation and effective management of marine ecosystems and biodiversity requires accurate species identification. This study classifies sea bamboo (Isis hippuris) specimens using DNA barcoding, a technique widely recognized for its speed, accuracy, and objectivity. This study examines the cytochrome c oxidase subunit I (COI) gene analysis for species identification. Isis hippuris was collected from two stations (coral and seagrass areas) of Tanjung Tiram Waters, South Konawe, Southeast Sulawesi. Genomic DNA was extracted from the base, main, and lateral stem of I. hippuris. Polymerase chain reaction (PCR) was used to amplify the mtDNA of I. hippuris with HCO2198 and LCO1490 primers. The highest quality PCR product based on the COI gene was chosen for sequencing analysis. The study revealed that COI gene analysis could only be performed on the base and main stem of the I. hippuris. Samples from coral and seagrass-coral areas on lateral stems were not further analyzed due to low concentration and purity values, which could potentially fail DNA sequencing. Each part of I. hippuris may have unique genetic differences. This study highlights the advantages of DNA sequencing in providing a unique genetic fingerprint for each species, enabling accurate species identification. This research provides insight into using DNA barcoding for sea bamboo species identification.

Characterization of the genetic composition and establishment of a core collection for the INERA Robusta coffee (Coffea canephora) field genebank from the Democratic Republic of Congo

Cultivation of Robusta coffee is likely to gain importance because of its high disease resistance and climate envelope. Robusta coffee genetic resources conserved in field genebanks can play an important role to further improve its cupping quality and other agronomic traits, but such Coffea canephora collections are limited and still poorly characterized. In this study, we characterized the genetic composition of the historically important but until recently neglected INERA Coffee Collection in Yangambi (the Democratic Republic of Congo). We used GBS to discover genome-wide genetic diversity, created and validated a novel multiplex amplicon sequencing (HiPlex) screening assay to genetically screen 730 coffee shrubs of the Yangambi Coffee Collection, grouped clonal material and delineated 263 accessions with unique genetic fingerprints. Comparison to reference material of three genetic origins revealed that the majority of the Yangambi accessions were assigned a ‘Lula’ cultivar origin, four accessions were assigned to Congolese subgroup A and nine accessions were most closely related to local wild accessions. About one-quarter of the accessions was likely derived from hybridization between these groups, which could result from seed-based propagation of the collection, breeding efforts, or natural cross-pollination. Parental analyses discovered eight preferentially used accessions, which may correspond to historically selected founders, or direct descendants thereof, whose seed material was once widely used to establish coffee plantations. Finally, two core collections were proposed using the maximization strategy (CC-I; 100 accessions) and genetic distance method (CC-X; 10 accessions). Our study demonstrates a method for the genetic characterization of Robusta coffee collections in general and contributes to the re-evaluation and exploration of the Robusta coffee genetic resources in the Democratic Republic of the Congo in particular.

Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken.

Understanding the genetic diversity of domestic chicken breeds under the impact of socio-cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1-M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200-300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio-cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure.

Study Genetic Distances Amonge Nine Okra, (Abelmoschus, esculentus) genotypes UsingTen ISSR markers

Ten from molecular marker ISSRs, (Inter, - Simple, Sequence, Repeats.) were used to find genetic, diversity, genetic* relationship, and DNA* fingerprint* of nine Okra (Abelmoschus esculentus) genotypes. Primers varied among them in giving unique DNA fingerprints, primers (UBC-809, HB12, and HBS10) gave a unique fingerprint for one genotype of okra, while primers (844A, UBC808) give unique fingerprint for four genotypes. High genetic distance was (0.722) between Egypt and Hasnawia while low genetic distance was (0.074) between Hasnawia and Lahluba. Cluster analysis (Phylogenetic tree) grouped studied genotypes in to two main cluster, the first large one included six genotype(Mosulia , Houseagrl, Khnisiraa ,Hasnawia ,Lahluba and Batra) and other small one includes three genotype (Soutl,Egypt and Zasco seed).ISSR marker could reveal genetic relationship in studied genotypes according to their origin, thus it gave an excellent tool to breeding programs help breeders .

Establishment and characterization of chemotherapy-enriched sphere-forming cells with stemness phenotypes as a new cell line (BAG50) of gastric carcinoma.

Gastric cancer is a malignancy with a high mortality rate worldwide. Cancer stem cells (CSCs) are a small subpopulation of tumor cells that possess the tumor-initiating ability, self-renewal capacity, and high resistance to conventional therapies. Due to the diversity and complexity of human tumors, new cell lines are urgently needed to supply clinically and physiologically relevant cancer models. Here, we report establishing a novel cell line (BAG50) with stemness properties. Chemotherapy-enriched sphere-forming cells with CSC properties isolated from a patient with GC were cultured in a serum-containing medium and passaged for up to 51 passages. The colony-forming ability and tumor-forming capacity of BAG50 cells were evaluated in vitro and in vivo. mRNA upregulation of stemness-related transcriptional factors using real-time PCR as well as expression of CSC markers using flow cytometry was investigated. Finally, STR profiling and chromosome studies were performed. BAG50 cells formed floating spheroid colonies in a serum-free medium. Subcutaneous injection of these cells generated xenograft tumors in nude mice. Pluripotency markers (SOX-2, OCT4, and Cripto-1) in them were upregulated compared with normal gastric cells. The majority of them expressed CSC markers of CD44, CD54, and EpCAM, and stemness marker of oct-4. STR profiling showed a unique DNA fingerprint. Karyotype also demonstrated multiple aneuploidies and chromosomal translocations. We suggested that the highly tumorigenic BAG50 cell line with stem cell-like phenotypes may provide a valuable in vitro tool to support new diagnostic, prognostic, and predictive biomarkers as well as the development of more effective treatment strategies.

Molecular characterization and genetic diversity analysis in Indian mustard (Brassica juncea L. Czern & Coss.) varieties using SSR markers.

In this study, we evaluated genetic diversity in a panel of 87 Indian mustard varieties using 200 genomic-SSR markers. A total of 189 SSRs resulted into positive amplification with 174 (92.06%) SSRs generating polymorphic products and 15 (7.94%) SSRs producing monomorphic amplicons. A total of 552 alleles were obtained and allele number varied from 2–6 with an average number of 3.17 alleles per SSR marker. The major allele frequency ranged from 0.29 (ENA23) to 0.92 (BrgMS841) with an average value of 0.58 per SSR locus. The polymorphic information content (PIC) value ranged from 0.10 (BrgMS841) to 0.68 (BrgMS519) with 0.39 as mean PIC value. The gene diversity per locus ranged from 0.13 (BrgMS841) to 0.72 (ENA23 & BrgMS519) with a mean value of 0.48 per SSR primer pair. Both Unweighted Neighbor Joining-based dendrogram and population structure analysis divided all the 87 varieties into two major groups/subpopulations. Analysis of molecular variance (AMOVA) inferred the presence of more genetic variation (98%) among individuals than among groups (2%). A total of 31 SSRs produced 36 unique alleles for 27 varieties which will serve as unique DNA-fingerprints for the identification and legal protection of these varieties. Further, the results obtained provided a deeper insight into the genetic structure of Indian mustard varieties in India and will assist in formulating future breeding strategies aimed at Indian mustard genetic improvement.

Single-cell analysis reveals heterogeneity of juvenile idiopathic arthritis fibroblast-like synoviocytes with implications for disease subtype

BackgroundFibroblast-like synoviocytes (FLS) play a crucial role in JIA pathogenesis; however, the mechanisms by which they contribute to disease progression are not well described. Previous studies demonstrated that rheumatoid arthritis FLS are heterogeneous, and subpopulations with transformed, aggressive phenotypes cause invasive and destructive disease activity. We employ single-cell RNA-sequencing (scRNA-seq) to investigate JIA FLS heterogeneity and gene expression that distinguishes JIA subtypes.MethodsJIA FLS cell lines from three persistent oligoarticular, three pre-extension oligoarticular, and three polyarticular subtypes were cultured. scRNA-seq was performed by Genewiz according to 10 × Genomics Chromium protocols. SeuratR package was used for QC, analysis, and exploration of data.ResultsFLS are heterogeneous and have characteristics of fibroblasts, chondrocytes, and smooth muscle cells. The chondrocyte-like subpopulation is the predominant cell type and percentages of this subpopulation increase with disease severity. Despite overlapping subpopulations, the chondrocyte-like cells have unique genetic fingerprints that distinguish between JIA subtypes. LRRC15, GREM1, and GREM2 are overexpressed in chondrocyte-like cells from persistent oligoarticular JIA FLS compared to pre-extension oligoarticular JIA FLS. S100A4, TIMP3, and NBL1 are overexpressed in pre-extension oligoarticular JIA FLS compared to polyarticular JIA FLS. CRLF1, MFAP5, and TNXB are overexpressed in persistent oligoarticular JIA FLS compared to polyarticular JIA FLS.ConclusionsWe found biologically relevant differences in gene expression between JIA subtypes that support a critical role for FLS in pathogenesis. We also demonstrate that gene expression within the chondrocyte-like subpopulation can be used to distinguish between these subtypes.

The Advent of Precision Immunology: Immunogenetics at the Center of Immune Cell Analysis in Health and Disease.

Adaptive immune cells (i.e., lymphocytes of the B and T lineage) are equipped with unique antigen receptors, which collectively form a highly diverse repertoire. Within the lymphocytes, the antigen receptor diversity is created at the DNA level through recombination processes in the immunoglobulin (IG) and T cell receptor (TR) genes that encode these receptors. This gives rise to an enormous immune repertoire (a.k.a. the "immunome") that can be studied in health and disease, both in a scientific and clinical context. In fact, the inherent distinctiveness of the IG/TR rearrangements on a per cell basis allows their usage as unique DNA fingerprints, which enables precision medicine, or for that matter "precision immunology." The field of (fundamental and translational) research on IG/TR repertoire diversity is the topic of the Immunogenetics volume in the Methods in Molecular Biology series.

Varietal identification and fingerprinting of Pearl Millet (Pennisetum glaucum L.) varieties and hybrid using morphological descriptors and SSR markers

Pearl Millet (Pennisetum glaucum) is the sixth most important cereal crop in the world. The genomic resources available in Pearl millet can be utilized for fingerprinting and screening of hybrids using SSR markers and will be helpful for the assessment of seed purity. Hence, the present study was focused on fingerprint popular pearl millet varieties and hybrids of Tamil Nadu for varietal identification and hybrid purity test. The varieties used for DNA fingerprinting were CO (Cu) 9, CO 10, Pearl Millet hybrid CO 9 along with the parents, A' line ICMA 93111A and R' line PT 6029-30. The morphological features were recorded to screen the cultivars. The Pearl millet hybrid CO 9 scored the highest value for more than four quantitative characters via., Number of productive tillers (4-6), Leaf blade length (60-68cm), Leaf blade width (4.0-4.5cm), number of nodes (8-10), and 1000 seed weight (13-14g) which is at par and comparable with the composite CO 10 and higher than that of the variety CO (Cu) 9. PCR was performed using 36 SSR primers to find out polymorphism among the varieties. The SSR markers ICMP3021 and PSMP2089 were able to selectively identify CO (Cu) 9 from the other varieties. Whereas, the SSR markers ICMP3018, PSMP2219, and PSMP2220 were used to distinguish CO 10 from the other varieties. Further, the CO10 variety produced additional alleles for all the markers due to its composite nature. Among the thirty-six SSR primers screened, none of them were found suitable to distinguish the TNAU hybrid CO 9 from its parents. The unique DNA fingerprints developed in the present study can be utilized for seed purity testing and varietal identification.

A preliminary study to identify and distinguish southern tropical populations of Ganoderma boninense from oil palm via mating assays, sequence data, and microsatellite markers

ABSTRACT Morphological studies suggest that the major pathogen causing basal stem rot of oil palm in Papua New Guinea and Solomon Islands is Ganoderma boninense. This study presents the first evidence for conspecificity of G. boninense from four countries where basal stem rot is prevalent. Seventy-three dikaryotic isolates of Ganoderma boninense from Indonesia, Malaysia, Papua New Guinea, and Solomon Islands were studied via mating tests, analyses of nuc internal transcribed spacer ITS1-5.8S-ITS2 sequences, and microsatellite genotyping. Sequence similarity in the ITS1-5.8S-ITS2 region was >99%, and all exotic isolates successfully mated with Papua New Guinea tester strains. Transfer of nuclei during mating was also confirmed via microsatellite markers for the first time in this species. Four microsatellite primers were used to generate evidence for 33 alleles in the four populations. All isolates studied had unique genetic fingerprints but alleles were also shared, suggesting gene flow. Heterozygosities were lower than expected in Indonesian and Papua New Guinea populations, consistent with the possibility of localized inbreeding.

A Theory of Biodiversity and Gene Evolution

The statement of theory: {Evolution of organisms and biodiversity depends mainly on gene evolution through the appearance of novel genes. Biodiversity results from the DNA modifications induced by visible and non-visible environmental effects, the variation of gene expression, stresses, mutation, and invasion of genetic materials. Each individual belongs to the same species of living organisms has its own identity of DNA fingerprint}. The principles of theory: Gene evolution depends mainly on gene duplication, a variety of environmental conditions, mutation, transposable elements, horizontal gene transfer (HGT). Also, de nove genes originated from non-coding DNA which mainly comes from retroviruses, exosome, micro-RNA, and invader nucleic acids from viruses, bacteria, or any parasite. Similarity and variations are the principles of life. In the same species, similarity produced from coding DNA while, individual variations arise from non-coding DNA. Aim and applications of theory: The main prediction of this theory is not only each individual of human beings have his unique DNA fingerprint, but also any individual in the same species has also a unique identity in DNA fingerprint. Any living organism acquires genetic materials through their intimate contacts with other organisms and environmental DNA. If the acquired genetic material reaches germ cells, it could transfer to the next generation giving new traits. Viruses considered the main source of genetic transformation in all living organisms. The genomic materials of some viruses could integrate inside the human genome like hepatitis B and HIV. The human genome has about 5 % viral genetic material, especially from retroviruses. This theory could explain the appearance of new individuals according to the transfer of genetic materials during intimate contact between different species and support many researchers who discovered new species. Also, this theory may explain and will answer different questions; why husband and wife after some time, nearly acquire some similarities? Why people in the same geographical area nearly have a similar pattern? Why don't siblings match their DNA fingerprint? Also, it explains the host-parasite relationship depending upon the transfer of DNA and RNA in between.

What Genes Can Tell: A Closer Look at Vestibular Schwannoma.

Comprehensive molecular profiling of radioresistant and cystic vestibular schwannoma (VS) subtypes. Our study utilized whole-exome sequencing (WES), RNA-sequencing (RNAseq), and correlated clinical data from 12 samples (2 samples of solid sporadic subtype, 8 with cystic changes, and 2 previously irradiated). Academic medical center. Patients diagnosed with VS who required surgical treatment. Inclusion: Cystic and radioresistant tumors matched to age and tumor volume, with solid sporadic VS samples as control; Exclusion: NF-2 patients. WES using custom probes for copy number analysis. A modified version of the Agilent Human Whole Exome sequencing hybrid capture system was used to process samples. Recurrent variants were identified and compared between groups. Leukocyte-derived DNA was utilized as internal control to reduce false-positives. Analysis of genetic landscape of VS subtypes (naive solid VS, cystic VS, and previously irradiated VS) by performing deep next-generation sequencing. WES data achieved a mean coverage of 202X and RNAseq generated an average of 74 million total reads. As a group, 25% of samples had 22q loss. Somatic analysis identified previously reported genes and multiple novel mutations across samples. Differential expression analysis of RNAseq data found significantly mutated genes such as COL6A3, CLMP, ART4, Lumican that were shared by both cystic VS and irradiated VS, but not seen in sporadic VS. Using WES we were able to demonstrate that cystic and irradiated samples are subtypes of VS with an increased mutation burden and a unique genetic fingerprint. We identified differences between the genomic and molecular profile of cystic VS and radioresistant VS. Our results help advance the understanding of the pathophysiology of these tumor subtypes and suggest possible molecular targets for novel treatment strategies.

Impact of fruit shape selection on genetic structure and diversity uncovered from genome-wide perfect SNPs genotyping in eggplant

The recently constructed eggplant genome provides an opportunity for genome-wide marker exploration to be used for variety identification and genetic analysis. SNPs with high density across the genome and genetic stability are suitable for DNA fingerprint and genetic analysis. In this study, we used the eggplant reference genome of line 63/7 and resequencing data of 45 unique lines to select 219 genome-wide perfect SNPs in the eggplant. The high-throughput SNP genotyping technique target SNP-seq was used to successfully validate the 219 SNPs across 377 eggplant varieties to establish the unique DNA fingerprint for each variety. In addition, we chose 36 SNPs as a core SNP set with the ability to differentiate 95% of 377 eggplant varieties. Model-based structure and principal component analysis suggested three major population groups and indicated a significant impact of long-term selection for fruit shape in eggplant varieties. Further genetic diversity analysis within the three population groups showed a considerably narrow genetic background in round- and oval-fruited eggplants. This could be a result of limited choices of varieties used for breeding of round- and oval-fruited eggplants in Asia, indicated by its low observed heterozygosity (Ho) value (0.152) and high inbreeding coefficient (0.442). Finally, a genome-wide association study based on the 219 SNPs identified five associated SNPs located near the SUN and OVATE homologs, which had conserved function in controlling the fruit shape. This study signals a risk of genetic erosion in the round- and oval-fruited eggplants and provides valuable information for future variety management and breeding programs.

Identification of elite Indian sugarcane varieties through DNA fingerprinting using genic microsatellite markers

Sugarcane is one of the important crops for sustainable economy and global energy security with high phenotypic polymorphism. Precise identification and characterization of plant genetic resources is one of the most essential aspects for breeding programs. Sugarcane popular hybrid varieties and genetic stocks routinely being used as a parent in hybridization program were included in the study. Molecular cataloguing was accomplished using a set of 70 primer pairs, of which ~ 39% were found to be robust polymorphic and unique in all the genotypes used. The number of DNA bands amplified by expressed sequenced tags derived simple sequence repeat (EST-SSR) primers ranged from 1 to 10 with an average of 5 bands per primer pair and their fragment size ranged between 50 and 1690 bp. Polymorphism information content (PIC) values were ranged from 0.17 to 1.00 with an average of 0.58. Unique DNA fingerprints of thirteen elite sugarcane varieties were generated with 27 polymorphic sugarcane specific EST-SSR markers. Analyses of DNA profiles produced by microsatellite markers showed the unique bands specific for individual variety. Generated DNA profiles would facilitate accurate variety identification in the perspective of protection of the breeder’s intellectual property rights, farmer’s rights and their purity testing. In addition, developed reliable DNA fingerprinting system will be able to track a potent parent genotype for breeding programs. The identified genotype specific and unique EST-SSR markers will be valuable for conservation and management of sugarcane genetic resources.

Relationships between Hybrid Performance and Genetic Distance Revealed by Morphological and Molecular Markers in Cowpea (Vignaunguiculata (L.) Walp)

The genetic diversity and relationships among six cowpea (Vigna unguiculata) genotypes were evaluated using 10 agro-morphological traits and two molecular marker systems ISSR and SRAP. The phenotypic distance (PD) among all genotypes was relatively high. ISSR markers were more efficient than SRAP with regards to polymorphism detection, average number of polymorphic-bands per primer (PB), resolving-power (RP), marker-index (MI) and polymorphism-information-content (PIC). ISSR and SRAP markers were generated cultivar or genotype specific unique DNA fingerprints able to identify the most diverse genotypes. The Dic genetic similarity ranged from 0.744 (P1 and P4) to 0.868 (P2 and P3). A positive correlation was found between ISSR and SRAP markers as well as between molecular markers and phenotypic markers. Based on phenotypic distance (PD) and genetic distance (GD), six parents of cowpea were crossed in half diallel fashion in order to determine combining ability to identify promising hybrids for ten traits including yield and its components. The both additive and non-additive effects of the controlling genes were involved in the inheritance of the traits studied. High broad-sense heritability estimates were obtained for all the traits as well as the narrow-sense heritability was larger than 0.60 in time to 50 % flowering, pod length, weight of pods per plant, weight of seeds per plant and total dry seed yield, so selection for these traits could be useful. The adequacy of additive-dominance model was fit for time to 50 % flowering, number of branches per plant, weight of pods per plant, weight of seeds per plant and total dry seed yield, while non-allelic gene interaction was observed for pod length, number of seeds per pod and pod diameter. The estimates of general combining effects revealed that P5 had the highest positive and significant values for number of pods per plant, weight of pods per plant, weight of seeds per pod and total dry seed yield while P1 exhibited the lowest negative and significant GCA for number of pods per plant, weight of pods per plant, weight of seeds per pod and total dry seed yield. The highly significant correlations were found between total dry seed yield and number of pods per plant (0.87), weight of pods per plant (0.95) and weight of seeds per plant (0.95). Mating designs used in this study were suitable for studying genetic parameters in cowpea. The high values of broad-sense and narrow-sense heritability indicated a good genetic variability for effective selection. The relationship between phenotypic and genotypic distance as well as the heterosis and SCA were estimated. Results indicated that the genetic distance was positive and/or negative and significantly correlated with some traits, while it was not significantly correlated with effects of heterosis and SCA for some other traits. Our results noted that knowledge about the genetic distance between parents can be used to predict hybrids performance.

Single Nucleotide Polymorphisms and Biochemical Markers As Complementary Tools To Characterize Hops ( Humulus lupulus L.) in Brewing Practice.

In brewing practice, the use of the appropriate hop variety is essential to produce consistent and high-quality beers. Yet, hop batches of the same variety cultivated in different geographical regions can display significant biochemical differences, resulting in specific taste- and aroma-related characteristics in beer. In this study, we illustrate the complementarity of genetic and biochemical fingerprinting methods to fully characterize hop batches. Using genotyping-by-sequencing (GBS), a set of 1 830 polymorphic single nucleotide polymorphism (SNP) markers generated 48 unique genetic fingerprints for a collection of 56 commercial hop varieties. Three groups of varieties, consisting of somaclonal variants, could not be further differentiated using this set of markers. Biochemical marker information offered added value to characterize hop samples from a given variety grown at different geographical locations. We demonstrate the power of combining genetic and biochemical fingerprints for quality control of hop batches in the brewing industry.

Clinical, Cytogenetic and Immunophenotype Distribution of Adult Acute Lymphoblastic Leukemia Among Latinos — a Report from a Large Single Institution Cohort in Southern California

Introduction:Acute Lymphoblastic Leukemia (ALL) is divided into Pre-B and T phenotypes depending on the progenitor cell giving rise to the malignant clone. This disease is the most common cancer in children while rare in adults. Interestingly, higher incidence rates and poorer outcomes have been reported in patients of Latin American ethnicity. This has been attributed to higher rates of Philadelphia-Like (Ph-like) ALL and increased incidence of high risk features such as absence of hyperdiploidy and absence of t(12;21). The current data among Latinos either exclusively looks at B cell precursor (BCP) ALL or does not distinguish between subtypes. Our study sets out to better define the phenotype of this subset of patients with traditionally poor outcomes.Methods:Our database consisted of 825 adult patients (ages 18-85 years) diagnosed with ALL from the City of Hope Comprehensive Cancer Center in Los Angeles, California. The population in Southern California has a particularly high number of Latinos due to its proximity to Mexico and Central America. According to the 2017 United States Census, 48.6% of the Los Angeles population is of Hispanic or Latino origin. Age at diagnosis, initial WBC count, CNS involvement, imumnophenotype, cytogenetics and rate of hematopoietic cell transplantation during therapy were assessed between ethnic groups. Multivariable Logistic Regression was done to determine the features that distinguish Latino patients for Non-Hispanic Whites.Results:57.4% of the patients were Latinos and 42.6% were Non-Hispanic Whites (NHWs), a distribution unique to the Los Angeles area and consistent with US census population data. BCP ALL was more common in Latinos when compared to NHWs with a Hazard Ratio of 5.13 (95% CI between 2.97-8.87). The presence of the t(9;22) or Philadelphia chromosome (Ph+) was more common in NHW patients. The Hazard Ratio for Ph+ ALL in NHWs was 0.53 (95% CI between 0.37-0.77) CNS involvement was more common in Latino patients and MLL was the only cytogenetic abnormality less common in NHWs. Normal Karyotype (NK), Complex and Others were all more common in Latino patients. No difference was found between WBC counts of Latinos and NHW. (Fig. 1).Discussion:ALL has been shown to have higher rates in the Latino population. Our results among adults ages 18-85 years old, demonstrated that this difference can be attributed to higher incidence of BCP ALL and not T-cell among Latinos. This is consistent with the previously reported higher rate of Ph-Like ALL and distinct molecular aberrations among Latinos. Our data shows that the rate of Ph+ ALL is higher in NHWs when compared to Latinos. This is a very interesting finding as the presence of Ph+ ALL and Ph-like ALL are mutually exclusive. Associations have been previously reported between Ph-like ALL and Latin American ethnicity. Although there are types of ALL that are neither Ph+ nor Ph-like this finding suggests a higher incidence of Ph-like ALL in Latinos. At the present time, standard cytogenetics do not include CRLF2, IKZF1 and other mutations found in Ph-like ALL. Complex cytogenetics and CNS involvement, both factors associated with poor prognosis, are most likely to present in a Latino patient. While the precise mechanism is unknown, our findings further support the hypothesis that a unique genetic fingerprint has led to development and outcomes of Ph-like ALL in Latinos. It is evident that this subset of unfavorable BCP ALL population needs special attention. More studies are imperative to further elucidate the mechanism behind Ph-like ALL and pinpoint the risk factors in the Latino population. [Display omitted] DisclosuresDouer:Spectrum: Consultancy; Amgen: Membership on an entity's Board of Directors or advisory committees; Pfizer: Honoraria; Jazz Pharmaceuticals: Consultancy; Gilled Sciences, Inc: Consultancy; Shire: Membership on an entity's Board of Directors or advisory committees.

AFLP-AFLP in silico-NGS approach reveals polymorphisms in repetitive elements in the malignant genome.

The increasing interest in exploring the human genome and identifying genetic risk factors contributing to the susceptibility to and outcome of diseases has supported the rapid development of genome-wide techniques. However, the large amount of obtained data requires extensive bioinformatics analysis. In this work, we established an approach combining amplified fragment length polymorphism (AFLP), AFLP in silico and next generation sequencing (NGS) methods to map the malignant genome of patients with chronic myeloid leukemia. We compared the unique DNA fingerprints of patients generated by the AFLP technique approach with those of healthy donors to identify AFLP markers associated with the disease and/or the response to treatment with imatinib, a tyrosine kinase inhibitor. Among the statistically significant AFLP markers selected for NGS analysis and virtual fingerprinting, we identified the sequences of three fragments in the region of DNA repeat element OldhAT1, LINE L1M7, LTR MER90, and satellite ALR/Alpha among repetitive elements, which may indicate a role of these non-coding repetitive sequences in hematological malignancy. SNPs leading to the presence/absence of these fragments were confirmed by Sanger sequencing. When evaluating the results of AFLP analysis for some fragments, we faced the frequently discussed size homoplasy, resulting in co-migration of non-identical AFLP fragments that may originate from an insertion/deletion, SNP, somatic mutation anywhere in the genome, or combination thereof. The AFLP–AFLP in silico–NGS procedure represents a smart alternative to microarrays and relatively expensive and bioinformatically challenging whole-genome sequencing to detect the association of variable regions of the human genome with diseases.

Microsatellite-based DNA Fingerprinting of Selected Grapevine Cultivars

Cultivar identification by ampelography is often difficult and is sensitive to environmental conditions, thus it can be problematic to distinguish between closely related cultivars. DNA fingerprinting offers an alternative method that is not influenced by the environment and is relatively easy to perform. However, discriminating between closely related individuals can be problematic if inadequate or insufficient markers are used. Following the estimation of null allele frequencies, an initial set of 35 microsatellite markers was reduced to 20 to generate unique DNA fingerprints for the majority of 111 different grape cultivars and breeding lines. Molecular evidence was utilised to evaluate the accuracy of the reported pedigrees for several cultivars bred in South Africa (SA). The use of markers linked to known downy mildew and powdery mildew resistance loci (Rpv3 and Ren3) provided information regarding the frequency of these resistance loci in the breeding material analysed.

Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers.

Durian (Durio zibethinus) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, HE = 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10−3. Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called “clones”, “varieties”, or “cultivars”. Such matters have a direct impact on the regulation and management of durian genetic resources in the region.