DNA Signature Research Articles

Prediction of response to immune checkpoint blockade in patients with metastatic colorectal cancer with microsatellite instability

Mismatch repair-deficient (dMMR) tumors displaying microsatellite instability (MSI) represent a paradigm for the success of immune checkpoint inhibitor (ICI)-based immunotherapy, particularly in patients with metastatic colorectal cancer (mCRC). However, a proportion of patients with dMMR/MSI mCRC exhibit resistance to ICI. Identification of tools predicting MSI mCRC patient response to ICI is required for the design of future strategies further improving this therapy. We combined high-throughput DNA and RNA sequencing of tumors from 116 patients with MSI mCRC treated with anti-programmed cell death protein 1 ± anti-cytotoxic T-lymphocyte-associated protein 4 of the NIPICOL phase II trial (C1, NCT03350126, discovery set) and the ImmunoMSI prospective cohort (C2, validation set). The DNA/RNA predictors whose status was significantly associated with ICI status of response in C1 were subsequently validated in C2. Primary endpoint was progression-free survival by immune RECIST (iRECIST) (iPFS). Analyses showed no impact of previously suggested DNA/RNA indicators of resistance to ICI, e.g. MSIsensor score, tumor mutational burden, or specific cellular and molecular tumoral contingents. By contrast, iPFS under ICI was shown in C1 and C2 to depend both on a multiplex MSI signature involving the mutations of 19 microsatellites hazard ratio cohort C2 (HRC2) = 3.63; 95% confidence interval (CI) 1.65-7.99; P= 1.4× 10-3] and the expression of a set of 182 RNA markers with a non-epithelial transforming growth factor beta (TGFB)-related desmoplastic orientation (HRC2= 1.75; 95% CI 1.03-2.98; P= 0.035). Both DNA and RNA signatures were independently predictive of iPFS. iPFS in patients with MSI mCRC can be predicted by simply analyzing the mutational status of DNA microsatellite-containing genes in epithelial tumor cells together with non-epithelial TGFB-related desmoplastic RNA markers.

OS-033 - Novel, high accuracy prediction models of hepatocellular carcinoma based on longitudinal data and cell-free DNA signatures

OS-033 - Novel, high accuracy prediction models of hepatocellular carcinoma based on longitudinal data and cell-free DNA signatures

Accuracy of Eye and Hair Color Prediction in Mexican Mestizos from Monterrey City Based on ForenSeqTM DNA Signature Prep.

Forensic genomic systems allow simultaneously analyzing identity informative (iiSNPs), ancestry informative (aiSNPs), and phenotype informative (piSNPs) genetic markers. Among these kits, the ForenSeq DNA Signature prep (Verogen) analyzes identity STRs and SNPs as well as 24 piSNPs from the HIrisPlex system to predict the hair and eye color. We report herein these 24 piSNPs in 88 samples from Monterrey City (Northeast, Mexico) based on the ForenSeq DNA Signature prep. Phenotypes were predicted by genotype results with both Universal Analysis Software (UAS) and the web tool of the Erasmus Medical Center (EMC). We observed predominantly brown eyes (96.5%) and black hair (75%) phenotypes, whereas blue eyes, and blond and red hair were not observed. Both UAS and EMC showed high performance in eye color prediction (p ≥ 96.6%), but a lower accuracy was observed for hair color prediction. Overall, UAS hair color predictions showed better performance and robustness than those obtained with the EMC web tool (when hair shade is excluded). Although we employed a threshold (p > 70%), we suggest using the EMC enhanced approach to avoid the exclusion of a high number of samples. Finally, although our results are helpful to employ these genomic tools to predict eye color, caution is suggested for hair color prediction in Latin American (admixed) populations such as those studied herein, principally when no black color is predicted.

Spiked nanorosette: A novel zinc oxide-gold textured nanostructure for impedance biosensing of target DNA signatures.

The creation of nanostructure is profound for the generation of nanobiosensors in several medical diagnosis. Here, we employed an aqueous hydrothermal route using Zinc-oxide (ZnO) and Gold (Au), which under optimal conditions formed an ultra-crystalline rose-like nanostructure textured with nanowires on the surface, coined as "spiked nanorosette." The spiked nanorosette structures was further characterized to possess crystallites of ZnO and Au grains with average sizes of 27.60 and 32.33nm, respectively. The intensity for both ZnO (002) and Au (111) planes of the nanocomposite was inferred to be controlled by fine-tuning the percentage of Au nanoparticles doped in the ZnO/Au matrix, as referred by X-ray diffraction analysis. The formation of ZnO/Au-hybrid nanorosettes were additionally verified by the distinct corresponding peaks from photoluminescence and X-ray photoelectron spectroscopy, supported by electrical validations. The biorecognition properties of the spiked nanorosettes were also examined using custom targeted and non-target DNA sequences. The DNA targeting capabilities of the nanostructures were analyzed by Fourier Transform Infrared and electrochemical impedance spectroscopy. The fabricated nanowire-embedded nanorosette exhibited a detection limit at the lower picomolar range of 1×10-12M, with high selectivity, stability and reproducibility and good linearity, under optimal conditions. Impedance-based techniques are more sensitive to the detection of nucleic acid molecule whereas this novel spiked nanorosette demonstrate promising attributes as excellent nanostructures for nanobiosensor developments and their potential future application for nucleic-acids or disease diagnostics.

Multimodal analysis of genome-wide methylation, copy number aberrations, and end motif signatures enhances detection of early-stage breast cancer.

Breast cancer causes the most cancer-related death in women and is the costliest cancer in the US regarding medical service and prescription drug expenses. Breast cancer screening is recommended by health authorities in the US, but current screening efforts are often compromised by high false positive rates. Liquid biopsy based on circulating tumor DNA (ctDNA) has emerged as a potential approach to screen for cancer. However, the detection of breast cancer, particularly in early stages, is challenging due to the low amount of ctDNA and heterogeneity of molecular subtypes. Here, we employed a multimodal approach, namely Screen for the Presence of Tumor by DNA Methylation and Size (SPOT-MAS), to simultaneously analyze multiple signatures of cell free DNA (cfDNA) in plasma samples of 239 nonmetastatic breast cancer patients and 278 healthy subjects. We identified distinct profiles of genome-wide methylation changes (GWM), copy number alterations (CNA), and 4-nucleotide oligomer (4-mer) end motifs (EM) in cfDNA of breast cancer patients. We further used all three signatures to construct a multi-featured machine learning model and showed that the combination model outperformed base models built from individual features, achieving an AUC of 0.91 (95% CI: 0.87-0.95), a sensitivity of 65% at 96% specificity. Our findings showed that a multimodal liquid biopsy assay based on analysis of cfDNA methylation, CNA and EM could enhance the accuracy for the detection of early- stage breast cancer.

Forensic identity SNPs: Characterisation of flanking region variation using massively parallel sequencing.

Single nucleotide polymorphisms (SNPs) can be analysed for identity or kinship applications in forensic genetics to either provide an adjunct to traditional STR typing or as a stand-alone approach. The advent of massively parallel sequencing technology (MPS) has provided a useful opportunity to more easily deploy SNP typing in a forensic context, given the ability to simultaneously amplify a large number of markers. Furthermore, MPS also provides valuable sequence data for the targeted regions, which enables the detection of any additional variation seen in the flanking regions of amplicons. In this study we genotyped 977 samples across five UK-relevant population groups (White British, East Asian, South Asian, North-East African and West African) for 94 identity-informative SNP markers using the ForenSeq DNA Signature Prep Kit. Examination of flanking region variation allowed for the identification of 158 additional alleles across all populations studied. Here we present allele frequencies for all 94 identity-informative SNPs, both including and excluding the flanking region sequence of these markers. We also present information on the configuration of these SNPs in the ForenSeq DNA Signature Prep Kit, including performance metrics for the markers and investigation of bioinformatic and chemistry-based discordances. Overall, the inclusion of flanking region variation in the analysing workflow for these markers reduced the average combined match probability 2175 times across all populations, with a maximum reduction of 675,000-fold in the West African population. The gain due to flanking region-based discrimination increased the heterozygosity of some loci above that of some of the least useful forensic STR loci; thus demonstrating the benefit of enhanced analysis of currently targeted SNP markers for forensic applications.

High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System

Sequence polymorphisms were characterized at 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), and 24 Y chromosomal STRs (Y-STRs) in 635 Northern Han Chinese with the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Since repeat region (RR) and flanking region (FR) variation can be detected by massively parallel sequencing (MPS), the increase in the number of unique alleles and the average of gene diversity was 78.18% and 3.51% between sequence and length, respectively. A total of 74 novel RR variants were identified at 33 STRs compared with STRSeq and previous studies, and 13 FR variants (rs1770275883, rs2053373277, rs2082557941, rs1925525766, rs1926380862, rs1569322793, rs2051848492, rs2051848696, rs2016239814, rs2053269960, rs2044518192, rs2044536444, and rs2089968964) were first submitted to dbSNP. Also, 99.94% of alleles were concordant between the ForenSeq DNA Signature Prep Kit and commercial CE kits. Discordance resulted from the low performance at D22S1045 and occasionally at DYS392, flanking region deletions at D7S820 and DXS10074, and the strict alignment algorithm at DXS7132. Null alleles at DYS505 and DYS448 and multialleles at DYS387S1a/b, DYS385a/b, DYS448, DYS505, DXS7132, and HPRTB were validated with other MPS and CE kits. Thus, a high-resolution sequence-based (SB) and length-based (LB) allele frequencies dataset from Northern Han Chinese has been established already. As expected, forensic parameters increased significantly on combined power of discrimination (PD) and combined power of exclusion (PE) at A-STRs, mildly on combined PD and combined mean exclusion chance (MEC) at X-STRs, and barely on discrimination capacity (DC) at Y-STRs. Additionally, MiSeq FGx quality metrics and MPS performance were evaluated in this study, which presented the high-quality of the dataset at 20 consecutive runs, such as ≥ 60% bases with a quality score of 20 or higher (%≥ Q20), > 60% of effective reads, > 2000 × of depth of coverage (DoC), ≥ 60% of allele coverage ratio (ACR) or heterozygote balance, ≥ 70% of inter-locus balance, and ≤ 0.4 of the absolute value of observed minus expected heterozygosity (|Hexp – Hobs|). In conclusion, MiSeq FGx can help us generate a high-resolution and high-quality dataset for human identification and population genetic studies.

Abstract CT088: Phase I/II study of the PARP inhibitor olaparib in combination with irinotecan in children with advanced malignancies: arm D of the AcSé-ESMART trial

Abstract Background: AcSé-ESMART is a proof-of-concept, phase I/II, platform trial, designed to explore targeted agents in a molecularly enriched relapsed/refractory pediatric population. Arm D was evaluating the PARP inhibitor (PARPi) olaparib (ola) in combination with irinotecan (iri). In contrast to other PARPi/chemotherapy combination studies, we opted for a prolonged course of PARPi and low dose irinotecan as sensitizer. The Phase I part previously established the recommended Phase II dose (RP2D) (Gatz ASCO 2019). This is the report of the Phase II part of the trial assessing the activity in two separate expansion cohorts: cohort 1: homologous recombination repair defect (HRD) and cohort 2: Ewing sarcoma (ES). Methods: Ola was administered orally twice daily at 90 mg/m2 on Days 1 to 10 and iri intravenously at 20 mg/m2 on Days 4 to 8 of a 21-day cycle. Activity assessment followed a Minimax Simon 2-stage design. Each cohort was to progress to the second stage (additional 9 patients) if 2 or more confirmed responses were observed in the first 16 patients. Patients treated in the Phase I part at the RP2D were counting towards the respective expansion cohorts. Results: Seventy patients (median age: 14 years, range 5-23) were included in the whole study, 67 received treatment; 27 patients were treated in the dose escalation part, including 10 at the RP2D (8 in cohort 1 and 2 in cohort 2). Both cohorts passed the 1st stage and a total of 24 and 26 patients were recruited to cohort 1 and 2, respectively. Main diagnoses in cohort 1 were sarcoma (n=10), brain tumor (n=9), neuroblastoma (n=4). In cohort 1, 15 of 24 patients were considered enriched based on molecular alteration at relapse (ATM n=6; BRCA1 n=2; DNA signature 3 n=3; FANCD2, CHEK2, FANCA, ATRX all n=1); all patients in cohort 2 had presence of a ES fusion (ESWR1::FLI1 n=22; EWSR1::ERG n=4). Median number of treatment cycles were 2, range 1;51 in cohort 1 and 1;32+ in cohort 2. In cohort 1, 3 patients had a partial response (PR) (pinealoblastoma, neuroblastoma, choroid plexus carcinoma; treated with 12, 51, 25 cycles), 1 patient an unconfirmed PR (rhabdomyosarcoma, 6 cycles) and 7 patients stable disease (SD) (2 prolonged with 6 and 8 cycles). In cohort 2, 1 patient had a complete response (10 cycles) and 1 a PR (32+ cycles), 7 patients had SD (3 prolonged with 6, 10, 16 cycles). Molecular enrichment did not predict response. Retrospective correlative analysis of the molecular profiling data and tumor tissue expression analysis are ongoing to identify predictive biomarkers for PARPi combination trials and data will be presented. Conclusions: Encouraging clinical benefit was observed with the protracted ola-iri schedule in a subset of patients. Current molecular hypothesis is insufficient for patient selection and better biomarkers are needed. Citation Format: Susanne A. Gatz, Pablo Berlanga, Baptiste Archambaud, Yassine Bouchoucha, Nicolas André, Nadege Corradini, Windy Rondof, Jonathan Rubino, Souad Nebchi, Antonin Marchais, Estelle Thebaud, Alba Rubio San Simón, Natasha K. van Eijkelenburg, Lynley V. Marshall, Anne-Sophie Defachelles, Adela Canyete, Stephane Ducassou, Guy Makin, Michela Casanova, Emilie De Carli, Arnaud Petit, Gwenael Le Teuff, Xavier Paoletti, Peter G. Mortimer, Gilles Vassal, Birgit Geoerger. Phase I/II study of the PARP inhibitor olaparib in combination with irinotecan in children with advanced malignancies: arm D of the AcSé-ESMART trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT088.

No evidence for a common blood microbiome based on a population study of 9,770 healthy humans

Human blood is conventionally considered sterile but recent studies suggest the presence of a blood microbiome in healthy individuals. Here we characterized the DNA signatures of microbes in the blood of 9,770 healthy individuals using sequencing data from multiple cohorts. After filtering for contaminants, we identified 117 microbial species in blood, some of which had DNA signatures of microbial replication. They were primarily commensals associated with the gut (n = 40), mouth (n = 32) and genitourinary tract (n = 18), and were distinct from pathogens detected in hospital blood cultures. No species were detected in 84% of individuals, while the remainder only had a median of one species. Less than 5% of individuals shared the same species, no co-occurrence patterns between different species were observed and no associations between host phenotypes and microbes were found. Overall, these results do not support the hypothesis of a consistent core microbiome endogenous to human blood. Rather, our findings support the transient and sporadic translocation of commensal microbes from other body sites into the bloodstream.

Comparative Analysis of the Interaction between the Antiviral Drug Umifenovir and Umifenovir Encapsulated in Phospholipids Micelles (Nanosome/Umifenovir) with dsDNA as a Model for Pharmacogenomic Analysis by Electrochemical Methods

In the present study, the electrochemical behavior of antiviral drug umifenovir (Umi) and umifenovir encapsulated in phospholipids micelles (nanosome/umifenovir, NUmi) were investigated for the first time on screen-printed electrodes modified by carbon nanotubes. We have shown that Umi can be electro oxidized around the potential of +0.4 V in the concentration range of 50–500 µM (R2 = 0.992). Non-overlapping signatures of DNA and umifenovir (10–150 µM) permit to register interaction between umifenovir (or umifenovir encapsulated in phospholipids micelles), purine, and pyrimidine heterocyclic bases of DNA separately. The type of interaction is most likely via electrostatic interactions and groove binding in drug-DNA formed complex, as was revealed based on the values of binding constants Kb and the cathodic shifts of oxidation potentials for heterocyclic bases with increasing Umi or NUmi concentration. The negative values of Gibbs free energy (ΔG) for all nucleobases confirm the process spontaneity. This study is the first one presenting the effect of antiviral drug umifenovir and umifenovir encapsulated in phospholipids micelles on dsDNA as a target of pharmacogenomics.

Application of a genetic signature of late GU toxicity in SCIMITAR, a Post-op SBRT trial.

Predictors of genitourinary toxicity after post-prostatectomy radiotherapy remain elusive. A previously defined germline DNA signature (PROSTOX) has shown predictive ability for late grade≥2 GU toxicity after intact prostate stereotactic body radiotherapy. We explore whether PROSTOX would predict toxicity among patients receiving post-prostatectomy SBRT on a phase II clinical trial.

Variability of 27 Autosomal STR Loci for the Population of the Republic of Belarus Based on the Mass Parallel Sequencing Data

Variability of 27 autosomal STR loci of the ForenSeq DNA Signature Prep Kit (Illumina) commercial panel was studied using the technology of mass parallel sequencing (MPS) in 733 unrelated individuals representing the population of the Republic of Belarus as well as a population base of MPS allele frequencies for expert probabilistic calculations in human identification and paternity establishment was evaluated. The agreement between genotypes obtained by MPS and capillary electrophoresis (CE) was 99.96%. The number of MPS alleles increased more than two times for eight loci (D12S391, D21S11, D2S1338, vWA, D3S1358, D8S1179, D13S317, D9S1122). Thirteen alleles detected were not included in the STRSeq BioProject catalog of the international online database STRbase 2.0. The random match probability of 27-locus MPS profiles decreased from 1.43 × 10–31 to 2.89 × 10–35, and the combined paternity index increased from 2.08 × 1010 to 3.25 × 1012 compared to CE data.

Conservation initiatives of Syngnathiformes species in the southern Philippines: What does the mitochondrial DNA signature tell us?

Abstract Mitochondrial DNA signatures based on the control region and 12S rRNA gene were used to assess the impact of conservation measures on the effective management of vulnerable Syngnathiformes (seahorses, pipefishes, and allies) species. Results from phylogenetic inference, polymorphism, neutrality indices, haplotype networks and microhabitat information may justify the establishment of distinct management units for different species. For smooth seahorses, Hippocampus kuda was identified as a species complex that formed three clusters with 20 haplotypes. Based on molecular data, these are the first records of Hippocampus capensis and Hippocampus casscsio in the Philippines. High haplotype diversity (h = 28; Hd = 0.943), yet low nucleotide diversity (Pi:0.18095) for polymorphism, suggests minor differences among haplotypes. Neutrality indices calculated using Tajima's D (−2.00774), with P < 0.05 and Fu's Fs (−11.645), were significant. However, both tests were negative, a signature of rapid population expansion from a small effective population size, which could be attributed to past heavy harvests and habitat destruction, as supported by local data. For pipefishes and their allies, there was high haplotype diversity (h = 22; Hd = 0.875) and low nucleotide diversity of Pi: 0.16671. However, neutrality indices calculated using Tajima's D (−1.68518) and Fu's Fs (11.549) were not significant, with P > 0.05, indicating a balancing selection for this population. Results reveal that the recent population expansion of seahorses proves that current conservation measures are effectively safeguarding populations, while balancing selection is maintaining genetic polymorphism in pipefishes and their relatives, making them resilient to changing environments. Moreover, as revealed by haplotype networks, intraspecific variation suggests distinct management for different species. In addition, underwater surveys show an essential association between microhabitats and species' survival, thus encouraging future initiatives regarding habitat protection, especially coral reefs, seagrass beds, sponge gardens, mangrove areas and estuaries.

Comparative genomic analysis of esophageal squamous cell carcinoma among different geographic regions.

Esophageal squamous cell carcinoma (ESCC) shows remarkable variation in incidence, survival, and risk factors. Although the genomic characteristics of ESCC have been extensively characterized, the genomic differences between different geographic regions remain unclear. In this study, we sequenced 111 patients with ESCC from northern (NC) and southern (SC) China, combined their data with those of 1081 cases from previous reports, and performed a comparative analysis among different regions. In total, 644 ESCC cases were collected from six geographic regions (NC, SC, Xinjiang, China [XJC], Japan [JP], Vietnam [VN], and Europe & America [EA]) as the discovery cohort. Validation cohort 1 included 437 patients with ESCC from the NC region. Validation cohort 2 included 54 and 57 patients from the NC and SC regions, respectively. Patients with ESCC in different regions had different genomic characteristics, including DNA signatures, tumor mutation burdens, significantly mutated genes (SMGs), altered signaling pathways, and genes associated with clinical features. Based on both the DNA mutation signature and the mutation profile of the most common genes, the NC and SC groups were clustered close together, followed by the JP, XJC, EA, and VN groups. Compared to patients with ESCC from SC, SMGs, including KMT2D, FAT1, and NOTCH1 were more frequently identified in patients with ESCC from NC. Furthermore, some genes (TDG and DNAH8) correlated with overall survival in completely opposite ways in patients with ESCC from different geographical regions. Our study provides insights into genomic differences in ESCC among different regions. These differences may be related to differences in environmental carcinogens, incidence, and survival.

Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis

Philippine native pigs (PhNP) are small black pigs domesticated in rural communities in the Philippines. They are valued locally for their various sociocultural roles. Recently, considerable literature has accumulated in the field of native pig production and marketing. However, there is limited research on the genetic diversity of PhNP. No previous study has investigated the evolutionary relatedness among native pigs from various islands and provinces in Luzon and the Visayas, Philippines. In addition, a much debated question is whether the PhNP were interbreeding with or even domesticated from endemic wild pigs. This study aims to clarify some of the uncertainties surrounding the identity and classification of PhNP based on mitochondrial DNA (mtDNA) signatures. Native pig samples (n = 157) were collected from 10 provinces in Luzon and the Visayas. Approximately 650 base pairs of the mtDNA D-loop region were sequenced and analyzed together with publicly available sequences. Pairwise-distance analysis showed genetic separation of North and South Luzon (SL) and the clustering of SL with Visayan pigs. Phylogenetic analysis showed that the PhNP clustered within 3 recognized Asian pig domestication centers: D2 (East Asia), D7 (Southeast Asia) and the Cordillera clade (sister to the Lanyu). We identified 19 haplotypes (1–38 samples each), forming 4 haplogroups, i.e., North Luzon, South Luzon and Visayas, Asian mix and the Cordillera cluster. No endemic wild pig mtDNA was detected in the native pig population, but evidence of interspecific hybridization was observed. This study showed that the Philippine native pigs have originated from at least 3 Sus scrofa lineage and that they were not domesticated from the endemic wild pigs of the Philippines.

Metabarcoding of eDNA for tracking the floral and geographical origins of bee honey

Authentic honey products have a high commercial value and are often falsified via adulteration. Metabarcoding of environmental DNA (eDNA) from bacterial, floral, and entomological sources has recently been proposed as a useful tool for identifying and authenticating floral and geographical origins of bee honey. In this study, eDNA metabarcoding was applied to reveal the bacterial, plant, and honey bee DNA signatures of 48 commercial honey products from six different geographical origins. Bacterial DNA composition in commercial honey showed different relative abundance of Paenibacillus and Bacillus in geographically different samples, and high abundance of Methylobacterium in chestnut honey implying potential use of bacterial DNA composition for honey authentication. Using the chloroplast trnL (UAA) as a DNA marker, floral origins of commercial honey were investigated. Based on floral DNA signatures, 12 monofloral honey samples were identified among the 45 samples tested. Targeted amplicon sequencing of cytochrome oxidase I (COI) gene from entomological DNA identified three different Apis mellifera sequence variants, specific to geographic origin of honey, suggesting that COI can be implemented as a DNA marker to trace the origin of honey. Therefore, the current study demonstrated the potential of eDNA based metabarcoding as a robust tool for evaluating commercial bee honey by exploring their floral and geographical origins.

A REVIEW ON MONKEY POX DISEASE

After the disastrous COVID-19 pandemic, now, monkey pox has spreaded its legs all over the world. Disease originated in Africa but its outbreak occurred in 89 countries since January 2022. As per the World Health Organization report, in between January 1, 2022, and August 10, 2022, 27,814 confirmed cases and 11 deaths occurred across 89 countries. Monkey pox is a viral infection which may occur in humans as well as in animals. Rope squirrel (Funisciurus spp.), Gambian pouched rat (Cricetomys gambianus), and Sooty mangabey monkey (Cercocebus atys) are suspected reservoir host for monkey pox. Its symptoms are similar to but milder than small pox. As orthopox viruses are morphologically identical to each other, Polymerase chain reaction is only test for detection of monkey pox-specific DNA signatures. There is no specific treatment for monkey pox infection but as monkey pox and small pox infections are hereditarily comparative so antiviral medications and antibodies created to safeguard against small pox are generally prescribed to prevent and treat monkey pox. One of the important measures for prevention from monkey pox is small pox vaccination to the individual and also to the healthy people in occupation who are at high risk of exposure except in immunocompromised individuals.

A method for early diagnosis of lung cancer from tumor originated DNA fragments using plasma cfDNA methylome and fragmentome profiles

Early detection is critical for minimizing mortality from cancer. Plasma cell-free DNA (cfDNA) contains the signatures of tumor DNA, allowing us to quantify the signature and diagnose early-stage tumors. Here, we report a novel tumor fragment quantification method, TOF (Tumor Originated Fragment) for the diagnosis of lung cancer by quantifying and analyzing both the plasma cfDNA methylation patterns and fragmentomic signatures. TOF utilizes the amount of ctDNA predicted from the methylation density information of each cfDNA read mapped on 6243 lung-tumor-specific CpG markers. The 6243 tumor-specific markers were derived from lung tumor tissues by comparing them with corresponding normal tissues and healthy blood from public methylation data. TOF also utilizes two cfDNA fragmentomic signatures: 1) the short fragment ratio, and 2) the 5′ end-motif profile. We used 298 plasma samples to analyze cfDNA signatures using enzymatic methyl-sequencing data from 201 lung cancer patients and 97 healthy controls. The TOF score showed 0.98 of the area under the curve in correctly classifying lung cancer from normal samples. The TOF score resolution was high enough to clearly differentiate even the early-stage non-small cell lung cancer patients from the healthy controls. The same was true for small cell lung cancer patients.

Forensic assessment on the application of a virtual pool of 30 Y-STRs

Ideally, a panel of Y short tandem repeats (Y-STRs) should include markers with gene diversity (GD) ≥ 0.70 to guarantee a highly accurate and precise individual identification in all forensic situations where Y loci analysis is necessary to support the findings obtained with autosomal STRs. Since not all markers in a multiplex set reach the optimal GD value, to achieve a greater discrimination capacity (DC), the number of Y-STRs has been gradually expanded also with the addition of rapidly mutating Y-STRs (RM Y-STRs). The present study has tried to assess, based on the genetic diversity of each Y-STR and the cumulative haplotype diversity provided by the single Y-STR panels tested, whether to increase in the number of Y-STRs is effective. For this purpose, three commercially available forensic kits - the PowerPlex® Y23 System, the Yfiler™ Plus PCR Amplification Kit, and the ForenSeq™ DNA Signature Prep Kit - that allow for the simultaneous analysis of 22–25 Y chromosome markers (including Y-STRs and RM Y-STRs) have been used for typing 115 unrelated male individuals from North-East Italy employing two capillary electrophoresis (Applied Biosystems® 3130 Genetic Analyzer and SeqStudio Genetic Analyzer for HID) and one massively parallel sequencing (MiSeq FGx™ Forensic Genomics System) systems. Forensic parameters, such as gene diversity, cumulative haplotype diversity (cHD), and discrimination capacity, were determined for the three Y-STRs kits and the virtual pool of 30 Y-STRs obtained by the overall combination of the Y-loci of the three kits. From the findings, it emerges that twelve markers in the virtual panel of 30 Y-STRs, are characterized by a value of GD ≥ 0.70, and of these, eleven included in the Yfiler™ Plus kit seem to be sufficient to ensure the achievement of haplotype resolution. In light of this, it does not appear necessary to expand the number of Y-STRs in the currently available kits.

Identification of culture-dependent microbes from mangroves reveals dominance of Bacillus including medically important species based on DNA signature

Abstract. Dechavez R, Calub ML, Genobata DR, Balacuit R, Jose R, Tabugo SR. 2022. Identification of culture-dependent microbes from mangroves reveals dominance of Bacillus including medically important species based on DNA signature. Biodiversitas 23: 5342-5350. Mangroves are among the most crucial plant hosts in the marine environment because of their notable role in the ecosystem and their benefits. Identification of plant-associated and culture-dependent microbes is key to having a rich reservoir of bioactive substances. DNA barcoding was done based on 16S rRNA gene and ITS region. In this study, seven (7) mangrove species were identified as hosts. Results show that most bacterial isolates from plant leaves were gram-positive bacteria belonging to phylum: Firmicutes and genus Bacillus. Phylogenetic inference reveals a diverse non-monophyletic group with medically and economically necessary species. Among the host plants, Sonneratia alba harbored the most species of bacteria and fungi. These include two medically important strains of B. cereus and B. thuringiensis and host-specific bacteria like B. altitudinis in S. alba, B. velezensis in Rhizophora apiculata, B. clausii in Avicennia marina and B. firmus in A. marina were revealed. Meanwhile, some bacteria like B. subtilis and B. megaterium were found in three host species and B. cereus was the most abundant being recorded in four host plants. Diverse strains of fungi, Aspergillus sp., A. nomiae, A. tubingensis and A. niger were also present. This study served as baseline data for future research on diversity and host ecology for possible drug discovery.