DNA Index Research Articles

Microsatellites used in forensics are in regions enriched for trait-associated variants

The 20 short tandem repeat (STR) loci of the combined DNA index system (CODIS) are the basis of the vastmajority of forensic genetics in the United States. One argument for permissive rules about the collection of CODIS genotypes is that the CODIS loci are thought to contain little information about ancestry or traits. However, in the past 20 years, a growing field has identified hundreds of thousands of genotype-trait associations. Here, we conduct a survey of the landscape of such associations surrounding the CODIS loci as compared with non-CODIS STRs. Although this study cannot establish or quantify associations between CODIS genotypes and phenotypes, we find that the regions around the CODIS loci are enriched for both known pathogenic variants (> 90th percentile) and for trait-associated SNPs identified in genome-wide association studies (GWAS) (≥ 95th percentile in 10kb and 100kb flanking regions), compared with other random sets of autosomal tetranucleotide-repeat STRs.

Prognostic and Pharmacotypic Heterogeneity of Hyperdiploidy in Childhood ALL.

High hyperdiploidy, the largest and favorable subtype of childhood ALL, exhibits significant biological and prognostic heterogeneity. However, factors contributing to the varied treatment response and the optimal definition of hyperdiploidy remain uncertain. We analyzed outcomes of patients treated on two consecutive frontline ALL protocols, using six different definitions of hyperdiploidy: chromosome number 51-67 (Chr51-67); DNA index (DI; DI1.16-1.6); United Kingdom ALL study group low-risk hyperdiploid, either trisomy of chromosomes 17 and 18 or +17 or +18 in the absence of +5 and +20; single trisomy of chromosome 18; double trisomy of chromosomes 4 and 10; and triple trisomy (TT) of chromosomes 4, 10, and 17. Additionally, we characterized ALL ex vivo pharmacotypes across eight main cytotoxic drugs. Among 1,096 patients analyzed, 915 had B-ALL and 634 had pharmacotyping performed. In univariate analysis, TT emerged as the most favorable criterion for event-free survival (EFS; 10-year EFS, 97.3% v 86.8%; P = .0003) and cumulative incidence of relapse (CIR; 10-year CIR, 1.4% v 8.8%; P = .002) compared with the remaining B-ALL. In multivariable analysis, accounting for patient numbers using the akaike information criterion (AIC), DI1.16-1.6 was the most favorable criterion, exhibiting the best AIC for both EFS (hazard ratio [HR], 0.45; 95% CI, 0.23 to 0.88) and CIR (HR, 0.45; 95% CI, 0.21 to 0.99). Hyperdiploidy and subgroups with favorable prognoses exhibited notable sensitivities to asparaginase and mercaptopurine. Specifically, asparaginase sensitivity was associated with trisomy of chromosomes 16 and 17, whereas mercaptopurine sensitivity was linked to gains of chromosomes 14 and 17. Among different definitions of hyperdiploid ALL, DI is optimal based on independent prognostic impact and also the large proportion of low-risk patients identified. Hyperdiploid ALL exhibited particular sensitivities to asparaginase and mercaptopurine, with chromosome-specific associations.

Association between HBV viral load and severity of liver inflammation in patients with chronic hepatitis B virus infection

Objective: To explore the relationship and dynamic changes between virological markers and hepatic pathological damage due to host anti-hepatitis B virus (HBV) immunity in the natural course of disease in chronic HBV infected patients. Methods: Two hundred and thirty-eight adult chronic HBV-infected patients who underwent liver biopsy from January 2016 to June 2022 in Taizhou Hospital, Zhejiang Province, were retrospectively selected. General clinical data such as age, gender, platelets, ALT, AST, albumin, HBV DNA, qHBsAg, HBeAg, and liver pathology diagnostic indexes such as the grade of liver necroinflammation and liver fibrotic stages of the patients were collected. The patients were grouped according to HBeAg status, and subgrouped according to different grades of liver necroinflammation and different HBV DNA loads. Statistical analyses were performed to compare the differences in HBV virologic marker levels between the groups, and the correlation between them and the indicators of hepatic inflammatory injury, such as ALT,AST, and the grade of liver necroinflammation in the patients. Results: The levels of HBV virological markers in HBeAg-positive patients with moderate or higher liver necroinflammatory grade (G≥2) were significantly lower than those with mild (no) liver necroinflammatory grade (G < 2) (P < 0.01); whereas the opposite trend was observed in HBeAg-negative patients, with the levels of HBV DNA, and qHBsAg in the G≥2 subgroup being significantly higher than those in the G < 2 subgroup (P < 0.01). Correspondingly, HBV DNA level and qHBsAg showed weak to moderately strong negative correlation with liver necroinflammatory grade and AST which was an indicator of hepatic inflammatory injury in HBeAg-positive patients (P < 0.05); whereas in HBeAg-negative patients, they showed weak to moderately strong positive correlation with hepatic inflammatory activity and ALT, AST (P < 0.001), in which qHBsAg showed only a weak positive correlation with patients' liver necroinflammatory grade (P = 0.003). Further subgroup analyses of HBeAg-positive patients according to whether the HBV DNA level was > 2×10(6) IU/ml showed weak to moderate negative correlations between HBV virological markers and liver necroinflammatory grade as well as ALT and AST in the subgroup of patients with HBV DNA > 2×10(6) IU/ml (P < 0.05); however, the negative correlation disappeared in patients who were still HBeAg positive and had HBV DNA ≤ 2×10(6) IU/ml. Moreover, HBV DNA and ALT, HBeAg and AST showed moderate positive correlation (P < 0.05). Conclusion: We speculate that the activation of host anti-HBV immunity can efficiently inhibit HBV replication by targeting the infected hepatocytes, but only in the early phase of disease progression in HBeAg positive patients with HBV DNA high (> 2×10(6) IU/ml).

Evaluation of factors leading to poor outcomes for pediatric acute lymphoblastic leukemia in Mexico: a multi-institutional report of 2,116 patients.

Pediatric acute lymphoblastic leukemia (ALL) survival rates in low- and middle-income countries are lower due to deficiencies in multilevel factors, including access to timely diagnosis, risk-stratified therapy, and comprehensive supportive care. This retrospective study aimed to analyze outcomes for pediatric ALL at 16 centers in Mexico. Patients <18 years of age with newly diagnosed B- and T-cell ALL treated between January 2011 and December 2019 were included. Clinical and biological characteristics and their association with outcomes were examined. Overall, 2,116 patients with a median age of 6.3 years were included. B-cell immunophenotype was identified in 1,889 (89.3%) patients. The median white blood cells at diagnosis were 11.2.5 × 103/mm3. CNS-1 status was reported in 1,810 (85.5%), CNS-2 in 67 (3.2%), and CNS-3 in 61 (2.9%). A total of 1,488 patients (70.4%) were classified as high-risk at diagnosis. However, in 52.5% (991/1,889) of patients with B-cell ALL, the reported risk group did not match the calculated risk group allocation based on National Cancer Institute (NCI) criteria. Fluorescence in situ hybridization (FISH) and PCR tests were performed for 407 (19.2%) and 736 (34.8%) patients, respectively. Minimal residual disease (MRD) during induction was performed in 1,158 patients (54.7%). The median follow-up was 3.7 years. During induction, 191 patients died (9.1%), and 45 patients (2.1%) experienced induction failure. A total of 365 deaths (17.3%) occurred, including 174 deaths after remission. Six percent (176) of patients abandoned treatment. The 5-year event-free survival (EFS) was 58.9% ± 1.7% for B-cell ALL and 47.4% ± 5.9% for T-cell ALL, while the 5-year overall survival (OS) was 67.5% ± 1.6% for B-cell ALL and 54.3% ± 0.6% for T-cell ALL. The 5-year cumulative incidence of central nervous system (CNS) relapse was 5.5% ± 0.6%. For the whole cohort, significantly higher outcomes were seen for patients aged 1-10 years, with DNA index >0.9, with hyperdiploid ALL, and without substantial treatment modifications. In multivariable analyses, age and Day 15 MRD continued to have a significant effect on EFS. Outcomes in this multi-institutional cohort describe poor outcomes, influenced by incomplete and inconsistent risk stratification, early toxic death, high on-treatment mortality, and high CNS relapse rate. Adopting comprehensive risk-stratification strategies, evidence-informed de-intensification for favorable-risk patients and optimized supportive care could improve outcomes.

Diagnostic Accuracy of Flow Cytometric DNA Index in Saudi Children with B Cell Acute Lymphoblastic Leukemia.

B cell Acute Lymphoblastic Leukemia (B-ALL) is one of the most common types of cancer diagnosed in children in Saudi Arabia. Cytogenetic investigations, including karyotyping and FISH, are used to determine the incidence and prognostic significance of chromosomal abnormalities in B-ALL. However, in ALL, accurate identification of the morphology of chromosomes is sometimes not achieved. Flow cytometric DI may have the advantage of being technically fast, using either fresh or frozen samples to correctly stratify the patient into the appropriate risk group for treatment. In this study, we evaluated the reliability and validity of using fixed samples instead of fresh samples to determine aneuploidy in cancer cells using a DNA index. The results of the DNA index obtained by flow cytometry were compared with those of conventional cytogenetic analysis to validate the accuracy. Fixed samples (n = 72) from children diagnosed with B-ALL at King Fahad Medical City in Riyadh between 2017 and 2019 were investigated. The results showed strong and statistically significant positive correlation between DNAI-FCM and conventional cytogenetic analysis (p = 0.000 < 0.01). The DNA index value by flow cytometry was proportional to the cytogenetic study in 94.36% (67) of the cases, while discrepancy was observed in 5.6% (four) cases. Our findings highlight the ability of the DNA index method to provide complementary information for the accurate diagnosis of aneuploidy in patients with B-ALL.

Mitochondrial modulation of amplified preconditioning influences of remote ischemia plus erythropoietin against skeletal muscle ischemia/reperfusion injury in rats

AimsSkeletal muscle ischemia and reperfusion (S-I/R) injury is relieved by interventions like remote ischemic preconditioning (RIPC). Here, we tested the hypothesis that simultaneous exposure to a minimal dose of erythropoietin (EPO) boosts the protection conferred by RIPC against S-I/R injury and concomitant mitochondrial oxidative and apoptotic defects. Main methodsS-I/R injury was induced in rats by 3-h right hindlimb ischemia followed by 3-h of reperfusion, whereas RIPC involved 3 brief consecutive I/R cycles of the contralateral hindlimb. Key findingsS-I/R injury caused (i) rises in serum lactate dehydrogenase and creatine kinase and falls in serum pyruvate, (ii) structural deformities like sarcoplasm vacuolations, segmental necrosis, and inflammatory cells infiltration, and (iii) decreased amplitude and increased duration of electromyography action potentials. These defects were partially ameliorated by RIPC and dose-dependently by EPO (500 or 5000 IU/kg). Further, greater repairs of S-I/R-evoked damages were seen after prior exposure to the combined RIPC/EPO-500 intervention. The latter also caused more effective (i) preservation of mitochondrial number (confocal microscopy assessed Mitotracker red staining) and function (citrate synthase activity), (ii) suppression of mitochondrial DNA damage and indices of oxidative stress and apoptosis (succinate dehydrogenase, myeloperoxidase, cardiolipin, and cytochrome c), (iii) preventing calcium and nitric oxide metabolites (NOx) accumulation and glycogen consumption, and (iv) upregulating EPO receptors (EPO-R) gene expression. Significancedual RIPC/EPO conditioning exceptionally mends structural, functional, and neuronal deficits caused by I/R injury and interrelated mitochondrial oxidative and apoptotic damage. Clinically, the utilization of relatively low EPO doses could minimize the hormone-related adverse effects.

Quantitative Evaluation of NOD2 Promoter Methylation Profiling in Colon Biopsy Samples from Ulcerative Colitis Patients and Non-Colitis Controls

Background: Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with evidence addressing the role of epigenetic changes. The intention of this study was to detect the association of DNA methylation levels of NOD2 gene with UC and to evaluate whether any of these changes might be a useful biomarker for detecting patients with UC.&#x0D; Methods: The methylation status of the promoter CpG islands (CGIs) of NOD2 gene was examined in the colonic mucosae of 15 cancer-free patients with UC and 15 age- and sex-matched healthy controls by the real-time quantitative multiplex-methylation specific PCR (QM-MSP) assay. Methylation-specific melting curve analysis (MS-MCA) were used to analyze the data.&#x0D; Results: The median unmethylated DNA index was significantly higher in cases compared to controls, and hypormethylation of NOD2 gene was significantly correlated with UC (Unmethylated DNA in UC vs. HC; 0.102±0.055 vs. 0.025±0.016, P = 0.000).&#x0D; Conclusion: The NOD2 gene that was differentially methylated in UC patients, providing new insights into the pathogenesis of UC, with a view to making steps toward the development of accurate biomarkers for diagnostic tools in UC.

A holistic approach for the selection of forensic DNA swabs

In the present study, we compared the performance of five different ISO 18385 certified forensic swabs for DNA sampling in practice over a time period of five months. Comparisons were made for DNA profiling success rates, measured as the percentage of CODIS (Combined DNA Index System) suitable profiles as well as for practical suitability during sampling at the scene, measured through a survey among collaborators. More than forty members of our crime scene investigation (CSI) unit took part in the test series and provided structured feedback concerning different aspects of swab handling. A total number of 1094 “touch” DNA samples have been subjected to DNA analysis. Swabs performed significantly different in terms of DNA profiling success rates. We also observed significant differences in DNA extraction efficiency between swabs. The evaluation by the collaborators of various aspects of handling differed significantly between swabs. We can assume that a more convenient handling decreases the risk of contamination or sample mislabelling and increases sampling efficiency and staff satisfaction. Our results demonstrate that the selection of disposable sampling devices such as forensic swabs for DNA sampling should be made based on a holistic approach. To be able to select the best performing swab for a given combination of CSI and DNA laboratory procedures, it might not be sufficient to only perform DNA extraction comparisons and trace sampling under controlled laboratory conditions.

Human background DNA on stones in an urban environment

Stones are frequently used as tools in criminal acts. In our department, around 5 % of all analysed crime scene related trace samples are contact or touch DNA traces swabbed from stones. These samples are primarily related to cases of damage to property and burglary. In court, questions can arise about DNA transfer and the persistence of background DNA not related to the respective crime. To shed some light on the question of how likely it is to detect human DNA as background DNA on stones from an urban environment, the surfaces of 108 stones sampled throughout the city of Bern, the Swiss capital, were swabbed. We detected a median quantity of 33 pg on the sampled stones. STR-profiles suitable for a CODIS (Combined DNA Index System) registration in the Swiss DNA database were established from 6.5 % of all sampled stone surfaces. For comparison, retrospective casework data analysis from routine crime scene samples demonstrates a success rate of 20.6 % for the establishment of CODIS-suitable DNA profiles from stones sampled for touch DNA. We further investigated how climatic conditions, location and properties of the stones affected the quantity and quality of the recovered DNA. In this study, we show that the quantity of the measurable DNA decreases significantly with increasing temperature. Furthermore, less DNA could be recovered from porous stones, compared to smooth ones.

Baseline and oxidatively damaged DNA in end-stage renal disease patients on varied hemodialysis regimens: a comet assay assessment.

Global estimates exhibit that one million people have end-stage renal disease, a disease-state characterized by irreversible loss of kidney structure and function, thus necessitating renal replacement therapy. The disease-state, oxidative stress, inflammatory responses, as well as the treatment procedure can have damaging effects on the genetic material. Therefore, the present study was carried out to investigate DNA damage (basal and oxidative) using the comet assay in peripheral blood leukocytes of patients (n = 200) with stage V Chronic Kidney Disease (on dialysis and those recommended but yet to initiate dialysis) and compare it to that in controls (n = 210). Basal DNA damage was significantly elevated (1.13x, p ≤ 0.001) in patients (46.23 ± 0.58% DNA in tail) compared to controls (40.85 ± 0.61% DNA in tail). Oxidative DNA damage was also significantly (p ≤ 0.001) higher in patients (9.18 ± 0.49 vs. 2.59 ± 0.19% tail DNA) compared to controls. Twice-a-week dialysis regimen patients had significantly elevated % tail DNA and Damage Index compared to the non-dialyzed and to the once-a-week dialysis group implying dialysis- induced mechanical stress and blood-dialyzer membrane interactions as probable contributors to elevated DNA damage. The present study with a statistically significant power implies higher disease-associated as well as maintenance therapy (hemodialysis)-induced basal and oxidatively damaged DNA, which if not repaired has the potential to initiate carcinogenesis. These findings mark the need for improvement and development of interventional therapies for delaying disease progression and associated co-morbidities so as to improve life expectancy of patients with kidney disease.

The antigen processing-associated transporter gene polymorphism: Role on gene and protein expression in HPV-infected pre-cancerous cervical lesion.

Human papillomavirus (HPV) is the major pathogen for cervical lesions. The evasion mechanism of the immune response and persistence of HPV infection can be influenced by polymorphisms (SNPs) in genes associated with transporter associated with antigen processing (TAP), which may change the peptide binding affinity or the TAP expression impacting the efficiency of peptide transport in the secretory pathway, and the presentation of peptides to cytotoxic T lymphocytes. This study aimed to evaluate the role of the TAP1 and TAP2 polymorphisms, TAP1, and TAP2 genes expressions, and protein levels in cervical cells presenting different degrees of pre-cancerous lesions in 296 immunocompetent women infected or not by HPV. TAP SNPs were genotyped by Sanger sequencing, and gene expression by real-time PCR. Aneuploidy was determined by DNA index using flow cytometry. TAP-1 and TAP-2 tissue expressions were evaluated by immunohistochemistry. The Asp697Gly SNP of TAP1 presented a risk for cellular aneuploidy (P=0.0244). HPV+ women had higher TAP-2 mRNA (P=0.0212) and protein (P<0.0001) levels. The TAP2D and TAP2E haplotypes were associated with the risk for aneuploidy and pre-cancerous lesions. In conclusion, nucleotide variability at the peptide binding region of peptide transporter genes, particularly of the TAP2 gene, may influence the HPV-peptide transportation from the cytosol to the endoplasmic reticulum, increasing the susceptibility to the development of high-grade cervical lesions.

Clinical impact of minimal residual disease and genetic subtypes on the prognosis of childhood acute lymphoblastic leukemia.

This study analyzed data from two consecutive protocols for children newly diagnosed with acute lymphoblastic leukemia (ALL) to determine the clinical impact of minimal/measurable residual disease (MRD) and recently identified tumor genetic subtypes. Genetic subtypes were determined by sequential approaches including DNA indexing, reverse transcriptase-polymerase chain reaction, multiplex ligation-dependent probe amplification, and RNA-sequencing. MRD was assessed by flow cytometry. The Taiwan Pediatric Oncology Group TPOG-ALL-2013 study enrolled patients who received MRD-directed therapy. The 5-year event-free survival (EFS) and overall survival rates in the 2013 cohort were 77.8% and 86.9% compared to those of the 2002 cohort, which were 62.4% and 76.5%. Among patients treated with MRD-guided therapy, those with ETV6-RUNX1 fusion and high hyperdiploidy had the highest 5-year EFS (91.4% and 89.6%, respectively). The addition of dasatinib improved outcomes in patients with BCR-ABL1 ALL. Recently identified subtypes like DUX4-rearranged, ZNF384-rearranged, MEF2D-rearranged, and PAX5alt subtypes were frequently positive for MRD after remission induction, and these patients consequently received intensified chemotherapy. Treatment intensification according to the MRD improved the outcomes of patients presenting DUX4 rearrangements. In high-risk or very-high-risk subtypes, the TPOG-ALL-2013 regimen did not confer significant improvements compared to TPOG-ALL-2002, and the outcomes of BCR-ABL1-like, MEF2D-rearranged, and KMT2A-rearranged ALL subtypes (in addition to those of T-cell ALL) were not sufficiently good. Novel agents or approaches are needed to improve the outcomes for these patients. The TPOG-ALL-2013 study yielded outcomes superior to those of patients treated in the preceding TPOG-ALL-2002 study. This study provides important data to inform the design of future clinical trials in Taiwan. MRD-directed therapy improved the outcomes for pediatric ALL, especially standard-risk patients. Genomic analyses and MRD might be used together for risk-directed therapy of childhood ALL. Our work provides important data to inform the design of future clinical trials in Taiwan.

Two-year review of firearm-related DNA casework evidence: A triage process to improve quality and efficiency

A two-year casework review of 617 firearm-related submissions representing 119 cases has provided a DNA testing triage template for prioritizing and processing touch evidence associated with firearms and firearm accessories. The evidence consisted of swabbings from various locations of a firearm or a firearm-related item, and each submission was assigned to one of the following descriptive groups: Body, Magazine, Trigger Area, Rifles, Gun Accessories, Barrel, Miscellaneous, or Revolvers. Ultimately, there were 543 submissions analyzed from DNA extraction through electrophoresis, and interpretable profiles evaluated to determine eligibility for entry into The Combined DNA Index System (CODIS). All samples were subjected to the same validated DNA technologies and methodologies used in the laboratory during the study’s February 2020 through February 2022 time period, allowing for direct comparison of data. A DNA profile, defined as the detection of at least one allele above the analytical threshold, was detected in 478 samples (88%). Interpretable profiles, defined as a DNA profile that, as a whole or in part, is deemed to be of sufficient quality that it is suitable for comparison to known DNA standards for the purpose of inclusion or exclusion, were observed in 287 samples (53%). In this sample set, there were 12 DNA profiles generated from nine different cases that were uploaded into CODIS, resulting in three CODIS hits. Additionally, there were 163 standards associated with these cases that were entered into CODIS. As a result of this extensive review, the data strongly supported modifications to both the Forensic Biology Unit’s firearm-related Case Submission Policy and the laboratory’s DNA process for triaging samples from firearms.

Biological evaluation, docking studies, and in silico ADME prediction of some pyrimidine and pyridine derivatives as potential EGFRWT and EGFRT790M inhibitors

Herein, a set of pyridine and pyrimidine derivatives were assessed for their impact on the cell cycle and apoptosis. Human breast cancer (MCF7), hepatocellular carcinoma (HEPG2), larynx cancer (HEP2), lung cancer (H460), colon cancers (HCT116 and Caco2), and hypopharyngeal cancer (FADU), and normal Vero cell lines were used. Compounds 8 and 14 displayed outstanding effects on the investigated cell lines and were further tested for their antioxidant activity in MCF7, H460, FADU, HEP2, HEPG2, HCT116, Caco2, and Vero cells by measuring superoxide dismutase (SOD), malondialdehyde content (MDA), reduced glutathione (GSH), and nitric oxide (NO) content. Besides, Annexin V-FITC apoptosis detection and cell cycle DNA index using the HEPG-2 cell line were established on both compounds as well. Furthermore, compounds 8 and 14 were assessed for their EGFR kinase (Wild and T790M) inhibitory activities, revealing eligible potential. Additionally, molecular docking, ADME, and SAR studies were carried out for the investigated candidates.

Large fragment Sanger sequencing identifies the newly encountered variant that caused null alleles in parentage testing.

Short tandem repeat (STR) is regarded as a crucial tool for personal identification as well as parentage testing. Thus, genotyping errors of STRs could have negative effects on the reliability of forensic identification. A null allele at the combined DNA index system (CODIS) core loci D2S1338 was found in a father-daughter pair with the AGCU Expressmarker 22 kit which was a commonly used commercial kit during our daily laboratory work. This null allele caused the father and daughter to not conform to the laws of inheritance, thus potentially generating erroneous conclusions that excluded parentage. To figure out the reason for this phenomenon, re-amplification with new primers and then large fragment Sanger sequencing was conducted. We found a G to G/T variation at the position which is fifty-nine bases away from the 3' end of the core repeat in both samples. This probably could be considered a novel variant at the primer binding region which had not been reported that resulted in the emergence of the null allele. We also found that there was more than one single-nucleotide polymorphism (SNP) with minor allele frequency (MAF) greater than 0.1 in the upstream and downstream sequences of D2S1338. When designing primers for amplification of D2S1338, the possible adverse results of these SNPs should be taken into account and avoided.

Study of DNA ploidy in newly diagnosed multiple myeloma by flow cytometry and its correlation with disease prognosis and outcome

Objectives: Multiparameter flow cytometry is increasingly being used in determining DNA content in several hematological malignancies where abnormal DNA ploidy is a useful prognostic marker. This study was done to analyze the DNA ploidy of plasma cells in multiple myeloma (MM) by flow cytometry and explore its role as a prognostic factor. Material and Methods: Propidium-iodide staining technique and gating based on light scatter properties were used. DNA index (DI) of the tumor sample was calculated as the ratio of the DNA content of the G0-G1 population of the myeloma cells with the normal control cells (lymphocytes) present in the same sample. Based on DI, ploidy was categorized as diploidy, hypodiploidy, and hyperdiploidy and the results were correlated with the clinical outcome. Results: Among 32 patients, none had hypodiploid DNA content, 8 (25%) patients had hyperdiploid DNA, and 24 (75%) patients had diploid DNA. There was no significant association between DI and international staging system staging (P = 0.68), Eastern Cooperative Oncology Group Performance Status (P = 0.59), and post-induction remission status (P = 0.10). The median overall survival (OS) in the study patients was 20 (CI 11.4–28.8) months and the median progression-free survival was not reached. There was no difference in the OS among patients with diploid MM and hyperdiploid MM (P = 0.84). Conclusion: Although hyperdiploid MM has been reported to have a better prognosis than diploid MM, we did not find any significant difference possibly due to the small sample size. Nevertheless, flow cytometry is a useful tool in DNA ploidy analysis and its role as a prognostic factor in various hematologic malignancies including MM can be further explored.

Darkness hormone or daylight hormone in women with systemic lupus erythematosus?

In this study, it was aimed to compare the effects of both melatonin and 25-hydroxyvitamin D3, defined as an immune modulator, on laboratory diagnostic criteria parameters and disease activity in patients with systemic lupus erythematosus (SLE). The study included 56 women with SLE and 40 healthy women (control group). Melatonin and 25-hydroxyvitamin D3 levels of patients and healthy individuals included in the study were examined. In addition, leukocytes, lymphocytes, platelets, C3, C4, anti-double-stranded DNA (Anti-dsDNA), antinuclear antibody, and SLE disease activity index (SLEDAI) were analyzed in women with SLE. Patients were divided into four subgroups according to SLEDAI. Melatonin and 25-hydroxyvitamin D3 levels of women with SLE were lower than healthy women (p < 0.001). Both melatonin and 25-hydroxyvitamin D3 levels were not correlated with laboratory diagnostic criteria parameters. Only 25-hydroxyvitamin D3 levels were correlated with leukocyte levels (p < 0.01). There was no significant difference between the melatonin levels of the subgroups. The 25-hydroxyvitamin D3 levels of the subgroup without disease activity were higher than levels of the subgroups with disease activity (p < 0.05). There was a negative correlation between SLEDAI score and 25-hydroxyvitamin D3 levels (p < 0.05). Women with SLE had lower melatonin and 25-hydroxyvitamin D3 levels than healthy women. On the other hand, parameters of laboratory diagnostic criteria of SLE disease were not related. Only 25-hydroxyvitamin D3 levels were inversely related leukocyte levels. SLE disease activity was not correlated with melatonin levels but negatively correlated with 25-hydroxyvitamin D3 levels. Key Points • Women with SLE have low levels of melatonin and 25-hydroxyvitamin D3. • Melatonin and 25-hydroxyvitamin D3 levels are not related to the laboratory diagnostic criteria parameters for SLE disease. • Low levels of melatonin and 25-hydroxyvitamin D3 may be a factor in the unbalanced immune system of SLE. • Supplementation of melatonin and 25-hydroxyvitamin D3 may be recommended for women patients with SLE.

Detailing the process of identifying and the outcomes of efforts to address lawfully "owed" DNA.

While missed DNA sample collection has been an identified problem for decades, there has yet to be a scholarly publication related to a large-scale effort to address lawfully "owed" DNA outside of a prison system. Lawfully owed DNA samples are DNA samples that legally should have been collected and entered into Combined DNA Index System (CODIS) based upon a qualifying offense but were not. As the first jurisdiction funded by the Bureau of Justice Assistance's Sexual Assault Kit Initiative to address lawfully owed DNA, this case study fills this knowledge gap by answering four key questions: What was the scope of the problem in this jurisdiction? What was the process by which individuals who owe were identified? What were the outcomes of these efforts? And what were the lessons learned and recommendations for other jurisdictions? Findings from this case study indicate widespread DNA sample collection issues in this jurisdiction, with nearly 15,000 identified as owing DNA over the span of approximately 7 years. Efforts to collect lawfully owed DNA samples from those who owe over a duration of approximately five and a half years have resulted in about one-fifth now being in CODIS, about 4% of these newly collected DNA profiles resulted in a forensic hit, and a quarter of those hits have resulted in a prosecution. This study serves as an important blueprint for other jurisdictions and underscores the importance of having effective policies and practices to help ensure that all who should lawfully have their DNA collected and uploaded into CODIS do.

Near-tetraploid T-cell acute lymphoblastic leukaemia in childhood: Results of the AIEOP-BFM ALL studies

BackgroundNear-tetraploidy–defined by DNA index 1.79–2.28 or 81–103 chromosomes–is a rare cytogenetic abnormality observed both in children and adults with T-cell acute lymphoblastic leukaemia (T-ALL) and its prognostic value is not yet determined. Patients and methodsWe report a retrospective study conducted in paediatric patients with newly diagnosed T-ALL treated in AIEOP-BFM ALL 2000 and 2009 studies. 31 near-tetraploid T-ALL patients (1.4%) are compared to T-ALL patients without near-tetraploidy. ResultsNear-tetraploid karyotype was associated with lower frequency of high-risk features: white blood cells count at diagnosis ≥100,000/μL (19.3% versus 41.0%, p-value < 0.001), PPR (13.3% versus 35.8%, p-value = 0.01) and minimal residual disease high-risk at the end of consolidation phase Induction B (4.03% versus 14.6%, p-value = 0.001). Complete remission was achieved at the end of induction phase (day 33) in 100% near-tetraploid T-ALL patients, compared to 93.2% T-ALL without near-tetraploidy. ConclusionOverall, we found that near-tetraploid T-ALL in newly diagnosed paediatric patients is associated with low-risk presenting features, with favourable treatment response and outcome.

Intraoperative Flow Cytometry for the Characterization of Gynecological Malignancies.

Simple SummaryAneuploidy and high proliferative potential are distinct features of neoplastic cells. Based on the established role of intraoperative flow cytometry in various types of cancer, the aim of the present study was to investigate its role in cancer cell identification during surgery for gynecological malignancies. The analysis time was 5–6 min per sample. A large percentage of tumors were characterized as aneuploid, while all tumor samples had a significantly high proliferation. Flow cytometry was performed in accordance with pathological evaluation, and the method had high sensitivity and specificity. Our results verify the value of intraoperative flow cytometry in gynecological malignancies, and warrant further investigation in multicenter studies.Cell-cycle analysis has shown the presence of aneuploidy to be associated with poor prognosis. We developed an innovative rapid cell-cycle analysis protocol (the Ioannina protocol) that permitted the intraoperative identification of neoplastic cells in a plethora of malignancies. Herein, we aimed to investigate the potential role of cell-cycle analysis in the intraoperative characterization of gynecological malignancies. Women who underwent surgery for gynecological malignancies in our institution over a three-year period were included in this study. Permanent section pathology evaluation was used as the gold standard for malignancy evaluation. Total accordance was observed between flow cytometry and pathology evaluation. In total, 21 aneuploid cancers were detected following DNA index calculation. Of these, 20 were hyperploid and 1 was hypoploid. In addition, tumor samples were characterized by a significantly lower percentage of cells in G0/G1, as well as an induced tumor index. The response time for flow cytometry to obtain results was 5–6 min per sample. It seems that flow cytometry analyses for intraoperative tumor evaluation can be safely expanded to gynecological malignancies. This is a novel practical approach that has been proven valuable in several tumor types to date, and also seems to be reliable for gynecological malignancies. Intraoperative flow cytometry is expected to be crucial in decisions of lymph node dissection in endometrial cancers, due to its rapid response regarding the tumor invasion of part or all of the myometrial thickness. In this way, the surgeon can quickly modify the plane of dissection. Our results warrant the further investigation of applying iFC in larger, multicenter studies.