DNA Sequence Variation Research Articles

Abstract 1735: DNA demethylating agents have cell type-specific effects on viability and BRCA2 alternative splicing

Abstract Introduction: BRCA2 is one of two principal tumor suppressors responsible for hereditary breast/ovarian cancer syndrome (HBOC). Patients with strong family histories of breast/ovarian cancer may carry BRCA2 DNA sequence variants of unknown clinical significance (VUSs). To evaluate which of these VUSs may contribute to cancer risk by altering splicing patterns, naturally occurring BRCA2 mRNA alternate splicing events have been extensively characterized, but it is not yet known which if any of these alternate splicing events plays a role in BRCA2 function. One variant lacking exon 3 (∆3), which maintains the full length translational reading frame, lacks sequence encoding EMSY and PALB binding domains as well as transactivation function. Previous work has shown that, while some VUSs associated with increased levels of ∆3 in lymphoblastoid cell lines are not pathogenic, germline deletions that eliminate BRCA2 exon 3 are associated with increased breast cancer risk. It is therefore of interest to characterize the factors that influence the frequency of naturally occurring BRCA2 exon 3-skipping, including cell types and therapies. DNA demethylating agents are used as cancer therapy to promote expression of tumor suppressor genes that may be epigenetically silenced in tumors. However, DNA methylation has been shown to be more frequent in exonic than intronic regions of protein-coding genes, suggesting that methylation may play a role in recruiting spliceosomal components to nascent pre-mRNA. It is therefore of interest to determine whether genomic demethylation affects alternative splicing patterns. Here, we explore whether BRCA2 exon 3 alternative splicing patterns are altered by demethylating agents. Methods: To determine whether DNA demethylating agents can alter the levels of ∆3, MCF7 and/or the non-cancer breast cell line MCF 10A was treated with 5-aza 2’-deoxycytidine (5-AzadC) or 5-Azacytidine (5-AzaC), and isoform-specific RT-PCR was used to compare relative levels of splice junctions containing or skipping exon 3. Results and Conclusions: 1) While the IC50 for both 5-AzadC and 5-AzaC in MCF 10A was similar (less than 1 μM), MCF7 showed considerably more resistance to 5-AzaC than 5-AzadC (IC50 of ≥ 5 μM vs ≤ 0.2 μM). 2) 5-AzaC treatment reduces the proportion of MCF 10A cultures in apoptosis but does not increase the proportion of viable cells, indicating it causes cell death by some other means. 3) While both 5-AzaC and 5-AzadC reduce relative levels of ∆3 in MCF7, 5-azadC does not reduce relative levels of ∆3 in MCF 10A, suggesting there may be a cell type-specific splicing response to genomic demethylation therapies. Citation Format: Jordan Werner, Hiba Siddiqui, Samiha Syed, Osman Khan, Servando Casillas Garabito, James D. Fackenthal. DNA demethylating agents have cell type-specific effects on viability and BRCA2 alternative splicing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1735.

Stochasticity in genetics and gene regulation.

Development from fertilized egg to functioning multi-cellular organism requires precision. There is no precision, and often no survival, without plasticity. Plasticity is conferred partly by stochastic variation, present inherently in all biological systems. Gene expression levels fluctuate ubiquitously through transcription, alternative splicing, translation and turnover. Small differences in gene expression are exploited to trigger early differentiation, conferring distinct function on selected individual cells and setting in motion regulatory interactions. Non-selected cells then acquire new functions along the spatio-temporal developmental trajectory. The differentiation process has many stochastic components. Meiotic segregation, mitochondrial partitioning, X-inactivation and the dynamic DNA binding of transcription factor assemblies-all exhibit randomness. Non-random X-inactivation generally signals deleterious X-linked mutations. Correct neural wiring, such as retina to brain, arises through repeated confirmatory activity of connections made randomly. In immune system development, both B-cell antibody generation and the emergence of balanced T-cell categories begin through stochastic trial and error followed by functional selection. Aberrant selection processes lead to immune dysfunction. DNA sequence variants also arise through stochastic events: some involving environmental fluctuation (radiation or presence of pollutants), or genetic repair system malfunction. The phenotypic outcome of mutations is also fluid. Mutations may be advantageous in some circumstances, deleterious in others. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.

The landscape of 8q24 cytoband in gastric cancer (Review).

Worldwide, gastric cancer (GC) is estimated to be the fifth most common type of cancer type in both sexes, ranking sixth for new cases, with >640,850 cases per year, and fourth in terms of mortality rate. Cancer presents numerical and structural alterations in chromosomes, often through gains and losses of regions. In GC, there are multiple genetic alterations, in which those located in cytoband 8q24 have been frequently described; essential genes are present in this cytoband, regulating the homeostasis of crucial biological processes, such as the MYC gene, which induces expression of selective genes to promote cell growth and proliferation. Conversely, DNA sequence variations can also occur when a single nucleotide in the genome sequence is altered, and this is termed a single nucleotide polymorphism (SNP). These alterations, which can serve as a biological marker, are present in at least 1% of the population and assist in identifying genes associated with GC. In the present review, 12 genes present in cytoband 8q24 related to GC (NSMCE2, PCAT1, CASC19, CASC8, CCAT2, PRNCR1, POU5F1B, PSCA, JRK, MYC, PVT1 and PTK2) are discussed. The PSCA gene was cited more frequently than others; it has four known SNPs associated with GC (rs2978980, rs2294008, rs2976392 and rs9297976). Thus, these SNPs should be further studied in different populations to determine their risk value in patients with GC.

Re‐examining the placement ofHydrostachysusing a large‐scale phylogenetic approach

AbstractPhylogenetic placement ofHydrostachys(Hydrostachyaceae) has long been enigmatic, the highly divergent morphology ofHydrostachyshaving prevented its confident placement in any clade of angiosperms. Phylogenetic placements using DNA sequence data have varied, with most studies suggesting a placement within Cornales. We conducted a large‐scale phylogenetic analysis based on nuclear and chloroplast datasets to re‐examine the relationships of the genus and assess the data sources and methodological factors that may cause alternative placements.Hydrostachyswas consistently recovered as a member of Cornales in all of our analyses based on 338 single‐copy nuclear genes and 78 chloroplast genes, but the divergentmatKsequences ofHydrostachysavailable in GenBank led to different phylogenetic placements. These highly divergent DNA sequences may make phylogenetic placement problematic, and other factors may also impact the placement, including taxon sampling, long‐branch attraction, incomplete lineage sorting, and potential artifacts (from contaminants, paralogs, or assembly errors) in the datasets.

Molecular surveillance of Kelch 13 polymorphisms in Plasmodium falciparum isolates from Kenya and Ethiopia

BackgroundTimely molecular surveillance of Plasmodium falciparum kelch 13 (k13) gene mutations is essential for monitoring the emergence and stemming the spread of artemisinin resistance. Widespread artemisinin resistance, as observed in Southeast Asia, would reverse significant gains that have been made against the malaria burden in Africa. The purpose of this study was to assess the prevalence of k13 polymorphisms in western Kenya and Ethiopia at sites representing varying transmission intensities between 2018 and 2022.MethodsDried blood spot samples collected through ongoing passive surveillance and malaria epidemiological studies, respectively, were investigated. The k13 gene was genotyped in P. falciparum isolates with high parasitaemia: 775 isolates from four sites in western Kenya (Homa Bay, Kakamega, Kisii, and Kombewa) and 319 isolates from five sites across Ethiopia (Arjo, Awash, Gambella, Dire Dawa, and Semera). DNA sequence variation and neutrality were analysed within each study site where mutant alleles were detected.ResultsSixteen Kelch13 haplotypes were detected in this study. Prevalence of nonsynonymous k13 mutations was low in both western Kenya (25/783, 3.19%) and Ethiopia (5/319, 1.57%) across the study period. Two WHO-validated mutations were detected: A675V in three isolates from Kenya and R622I in four isolates from Ethiopia. Seventeen samples from Kenya carried synonymous mutations (2.17%). No synonymous mutations were detected in Ethiopia. Genetic variation analyses and tests of neutrality further suggest an excess of low frequency polymorphisms in each study site. Fu and Li’s F test statistic in Semera was 0.48 (P > 0.05), suggesting potential population selection of R622I, which appeared at a relatively high frequency (3/22, 13.04%).ConclusionsThis study presents an updated report on the low frequency of k13 mutations in western Kenya and Ethiopia. The WHO-validated R622I mutation, which has previously only been reported along the north-west border of Ethiopia, appeared in four isolates collected from eastern Ethiopia. The rapid expansion of R622I across Ethiopia signals the need for enhanced monitoring of the spread of drug-resistant P. falciparum parasites in East Africa. Although ACT remains currently efficacious in the study areas, continued surveillance is necessary to detect early indicators of artemisinin partial resistance.

Association of Poor Oral Health With Neuroimaging Markers of White Matter Injury in Middle-Aged Participants in the UK Biobank.

Poor oral health is a modifiable risk factor that is associated with clinically observed cardiovascular disease. However, the relationship between oral and brain health is not well understood. We tested the hypothesis that poor oral health is associated with worse neuroimaging brain health profiles in middle-aged persons without stroke or dementia. We performed a 2-stage cross-sectional neuroimaging study using UK Biobank data. First, we tested for association between self-reported poor oral health and MRI neuroimaging markers of brain health. Second, we used Mendelian randomization (MR) analyses to test for association between genetically determined poor oral health and the same neuroimaging markers. Poor oral health was defined as the presence of dentures or loose teeth. As instruments for the MR analysis, we used 116 independent DNA sequence variants linked to increased composite risk of dentures or teeth that are decayed, missing, or filled. Neuroimaging markers of brain health included white matter hyperintensity (WMH) volume and aggregate measures of fractional anisotropy (FA) and mean diffusivity (MD), 2 metrics indicative of white matter tract disintegrity obtained through diffusion tensor imaging across 48 brain regions. We included 40,175 persons (mean age 55 years, female sex 53%) enrolled from 2006 to 2010, who underwent a dedicated research brain MRI between 2014 and 2016. Among participants, 5,470 (14%) had poor oral health. Poor oral health was associated with a 9% increase in WMH volume (β = 0.09, SD = 0.014, p < 0.001), 10% change in aggregate FA score (β = 0.10, SD = 0.013, p < 0.001), and 5% change in aggregate MD score (β = 0.05, SD = 0.013, p < 0.001). Genetically determined poor oral health was associated with a 30% increase in WMH volume (β = 0.30, SD = 0.06, p < 0.001), 43% change in aggregate FA score (β = 0.43, SD = 0.06, p < 0.001), and 10% change in aggregate MD score (β = 0.10, SD = 0.03, p < 0.01). Among middle age Britons without stroke or dementia, poor oral health was associated with worse neuroimaging brain health profiles. Genetic analyses confirmed these associations, supporting a potentially causal association. Because the neuroimaging markers evaluated in this study precede and are established risk factors of stroke and dementia, our results suggest that oral health, an easily modifiable process, may be a promising target for very early interventions focused on improving brain health.

Genetic and functional variants of the TBX20 gene promoter in dilated cardiomyopathy.

Dilated cardiomyopathy (DCM) is a major cause of heart failure and sudden cardiac death. As DCM is a genetically heterogeneous disease, genetic variants of cardiac transcription factor genes may play an important role. Transcription factor TBX20, an indispensable factor in normal heart development, is involved in the regulation of cardiac structure and function. Although the TBX20 gene is associated with the occurrence and development of DCM, the influence of genetic variants of the TBX20 gene promoter region on DCM has not been reported. We conducted a case-control study consisting of 107 DCM patients and 210 healthy controls. Genetic variants within TBX20 gene promoter region were identified using sequencing techniques and were functionally analyzed by dual-luciferase reporting assay. Electrophoretic mobility shift assay (EMSA) was used to investigate DNA-protein interactions. In this study cohort (n = 317), we identified eight variants within TBX20 gene promoter. One novel DNA sequence variants (DSV) (g.4275G>T) and four single-nucleotide polymorphisms (SNPs) [g.4169G>A (rs1263874255), g.4949C>T (rs1191745927), g.5114G>A (rs112076877), g.5252C>T (rs1356932911)] were identified in DCM patients, but in none of controls. Among them, the DSV (g.4275G>T) and three SNPs [g.4949C>T (rs1191745927), g.5114G>A (rs112076877) and g.5252C>T (rs1356932911)] significantly altered the transcription activity of TBX20 gene promoter by dual-luciferase reporting assay (p < 0.05). Further, EMSA assay indicated that the DSV (g.4275G>T) and three SNPs [g.4949C>T (rs1191745927), g.5114G>A (rs112076877) and g.5252C>T (rs1356932911)] affected the binding of transcription factors. These data indicate that the DSV (g.4275G>T) and three SNPs [g.4949C>T (rs1191745927), g.5114G>A (rs112076877) and g.5252C>T (rs1356932911)] increase transcription activity of TBX20 gene promoter in both HEK-293 and neonatal rat cardiomyocytes (NRCMs) cell lines by affecting the binding of transcription factors. But the mechanism remains to be verified invivo.

RFLP-inator: interactive web platform for in silico simulation and complementary tools of the PCR-RFLP technique.

Polymerase chain reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) is an established molecular biology technique leveraging DNA sequence variability for organism identification, genetic disease detection, biodiversity analysis, etc. Traditional PCR-RFLP requires wet-laboratory procedures that can result in technical errors, procedural challenges, and financial costs. With the aim of providing an accessible and efficient PCR-RFLP technique complement, we introduce RFLP-inator. This is a comprehensive web-based platform developed in R using the package Shiny, which simulates the PCR-RFLP technique, integrates analysis capabilities, and offers complementary tools for both pre- and post-evaluation of in vitro results. We developed the RFLP-inator's algorithm independently and our platform offers seven dynamic tools: RFLP simulator, Pattern identifier, Enzyme selector, RFLP analyzer, Multiplex PCR, Restriction map maker, and Gel plotter. Moreover, the software includes a restriction pattern database of more than 250,000 sequences of the bacterial 16S rRNA gene. We successfully validated the core tools against published research findings. This new platform is open access and user-friendly, offering a valuable resource for researchers, educators, and students specializing in molecular genetics. RFLP-inator not only streamlines RFLP technique application but also supports pedagogical efforts in genetics, illustrating its utility and reliability. The software is available for free at https://kodebio.shinyapps.io/RFLP-inator/.

Epigenetic variation mediated by lncRNAs accounts for adaptive genomic differentiation of the endemic blue mussel Mytiluschilensis

Epigenetic variation affects gene expression without altering the underlying DNA sequence of genes controlling ecologically relevant phenotypes through different mechanisms, one of which is long non-coding RNAs (lncRNAs). This study identified and evaluated the gene expression of lncRNAs in the gill and mantle tissues of Mytilus chilensis individuals from two ecologically different sites: Cochamó (41°S) and Yaldad (43°S), southern Chile, both impacted by climatic-related conditions and by mussel farming given their use as seedbeds. Sequences identified as lncRNAs exhibited tissue-specific differences, mapping to 3.54 % of the gill transcriptome and 1.96 % of the mantle transcriptome, representing an average of 2.76 % of the whole transcriptome. Using a high fold change value (≥|100|), we identified 43 and 47 differentially expressed lncRNAs (DE-lncRNAs) in the gill and mantle tissue of individuals sampled from Cochamó and 21 and 17 in the gill and mantle tissue of individuals sampled from Yaldad. Location-specific DE-lncRNAs were also detected in Cochamó (65) and Yaldad (94) samples. Via analysis of the differential expression of neighboring protein-coding genes, we identified enriched GO terms related to metabolic, genetic, and environmental information processing and immune system functions, reflecting how the impact of local ecological conditions may influence the M. chilensis (epi)genome expression. These DE-lncRNAs represent complementary biomarkers to DNA sequence variation for maintaining adaptive differences and phenotypic plasticity to cope with natural and human-driven perturbations.

Genetic structure and demographic history of whiting Merlangius merlangus (Linnaeus, 1758) populations distributed in Turkey inferred from variation in mitochondrial DNA sequences

The genetic diversity, structure, and demographic history of the economically important and overfished Gadidae species Merlangius merlangus were investigated using the non-coding mitochondrial Control Region (CR) from five different sites in the Sea of Marmara and the Black Sea in Turkey. The populations of M. merlangus were found to be genetically diverse, with 14 haplotypes and 15 polymorphic regions. The overall haploid diversity was 0.910 ± 0.024, and the nucleotide diversity was 0.003± 0.0003. Genetic distances between populations varied between 0.13% and 8.02%, while genetic distances within M. merlangus populations varied between 0.09% and 0.42%. Principle Coordinates Analysis showed that Marmara, Black Sea, and Karadeniz Ereğli populations were clearly separated. Pairwise FST values varied from 0.12 to 0.69, highlighting high genetic variation among populations. The Black Sea and Marmara lineages of M. merlangus diverged from the North Sea lineage 1.65 (1.08-2.29) mya, whereas the separation between the Atlantic lineage occurred about 0.84 (0.51-1.2) mya. The recent expansion of the whiting population was identified through neutrality tests and mismatch distribution analyses. This study provides important insight into the genetic structure, conservation, and management of this species.

New Assay Technology and Utility of Peripheral Blood Vs Bone Marrow for Molecular MRD in AML and MDS

Background Rare tumor-specific mutations in patient samples serve as excellent markers to monitor the course of malignant disease and responses to therapy in clinical routine, and improved assay techniques are needed for broad adoption. We describe herein - superRCA assays - which provides for rapid and highly specific detection of DNA sequence variants present at very low frequencies in DNA samples using a standard flow cytometer for readout. We demonstrate and compare the assay against ddPCR for precise, ultra-sensitive detection of single-nucleotide mutant sequences from malignant cells to follow the course of AML and MDS patients following allogeneic stem cell transplantation, both in bone marrow and peripheral blood. Methods This study is based on patient material from the Nordic MDS study NMDSG14B (NCT02872662)and AML samples from the U-CAN biobank. The patients in this retrospective study have all previously undergone sequencing (TruSight panel, Illumina) upon diagnosis, after which patient specific driver mutations (1-4 per patient) has been chosen and analyzed longitudinally to monitor molecular MRD using ddPCR (Bio-Rad). These longitudinal samples were re-analyzed using superRCA mutation assays (Rarity Bioscience), a novel and ultra-sensitive technique for mutation detection using flow cytometer for readout. Both quarterly bone marrow aspirates and monthly peripheral blood samples post allogeneic stem cell transplantation were included to investigate to what extent frequent blood derived molecular MRD gives equivalent relapse information as bone marrow. For each mutation, sensitivity was assessed through serial dilution and wild type control, with the limit of detection calculated as Mean(wt)+3*SD(wt). Samples were analyzed in duplicates or triplicates and sample to sample variation was calculated as SD/Mean. Resul ts A total of 22 relapse patients and 21 different mutations were analyzed, covering single nucleotide variants, insertions, deletions, as well as mutations with very high GC in ASXL1 and SRSF2. The analysis demonstrating lower background and limit of detection for the superRCA assays compared to the equivalent ddPCR data. With spike-in dilution series, we demonstrated the superRCA assay could detect single point mutations as low as 1 in 100,000 with the flow cytometer readout. Mean background for superRCA was 0,0016% in wild type controls, and mean limit of detection was 0,0023%. From available serial dilutions, the mean sample to sample variation (CV) at 0,016% was 22,87% and 29,32% at 0,001% dilution. In longitudinal sample analysis of relapse patients, superRCA assay detected remaining mutations after initial treatment and clearly revealed the remaining malignant clone, subsequently leading to a relapse. The superRCA assay also demonstrated the feasibility of detecting corresponding leukemia mutations in the PBMCs when such mutations were present in bone marrow. Conclusions The data shows comparable mutant allele frequency results between superRCA and ddPCR upon diagnosis and relapse. The data further demonstrates superRCA mutation assays for the selected driver mutations can reach to very low limit of detection and increasing mutations could be detected in both blood and bone marrow predicting the relapse of MDS post transplantation in clinical samples. The low detection limit and high precision of superRCA are consequences of the highly selective genotyping of the repeated target sequences in combination with high input capacity and the large numbers of products that may be conveniently analyzed by flow cytometry. To further study the utility of using peripheral blood for molecular MRD in MDS and AML patients, more data is needed and studies are ongoing.

Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States.

Multivalent binding of CTCF to variable DNA sequences is thought to underlie its ability to mediate diverse cellular functions. CTCF typically binds a 20 base-pair consensus DNA sequence, but the full diversity of CTCF binding sites (CBS) within the genome has not been interrogated. We assessed CTCF occupancy in cultured cortical neurons and observed surprisingly that ~ 22% of CBS lack the consensus CTCF motif. We report here that sequence diversity at most of these atypical CBS involves degeneracy at specific nucleotide positions within the consensus CTCF motif, which likely affect the binding of CTCF zinc fingers 6 and 7. This mode of atypical CTCF binding defines most CBS at gene promoters, as well as CBS that are dynamically altered during neural differentiation and following neuronal stimulation, revealing how atypical CTCF binding could influence gene activity. Dynamic CBS are distributed both within and outside loop anchors and TAD boundaries, suggesting both looping-dependent and independent roles for CTCF. Finally, we describe a second mode of atypical CTCF binding to DNA sequences that are completely unrelated to the consensus CTCF motif, which are enriched within the bodies of tissue-specific genes. These tissue-specific atypical CBS are also enriched in H3K27ac, which marks cis-regulatory elements within chromatin, including enhancers. Overall, these results indicate how atypical CBS could dynamically regulate gene activity patterns during differentiation, development, and in response to environmental cues.

Abstract 12761: Pathogenic Genetic Variants in Patients With Heart Transplant Due to Ischemic and Non-Ischemic Cardiomyopathy

Introduction: Current clinical guidelines recommend offering genetic testing to all patients diagnosed with non-ischemic cardiomyopathy (NICM), particularly in patients with a strong family history. The utility of genetic testing more broadly in patients with end-stage heart failure requiring heart transplant (HT) is unknown. Hypothesis: Among patients with HT, prevalence of cardiovascular disease (CVD)-associated pathogenic/likely pathogenic (P/LP) variants is higher in those with NICM than those with ischemic cardiomyopathy (ICM). Methods: We performed targeted DNA sequencing of 120 mendelian CVD genes in 124 consented patients with a HT, enrolled in the Vanderbilt Cardiac Catheterization Lab Cohort between 2003 and 2021. DNA sequence variation was annotated as P/LP based on ACMG criteria. Results: Out of 124 participants with HT, 70 had NICM and 51 had ICM. 22.8% of the NICM group harbored a P/LP variant in TTN (n=5), LMNA (5), MYH7 (1), RYR2 (1), RBM20 (1), COL1A2 (1), PKP2 (1), and CASQ2 (1). 19.6% of ICM participants harbored a P/LP variant in LDLR (2), RYR2 (1), TTN (1), SDHA (1), MYH7 (1), SGCD (1), MYL3 (1), CASQ2 (1), and COL1A2 (1). In NICM and ICM patients with a P/LP variant, 94% and 100% had a family history of CVD, respectively. By comparison in those without a P/LP variant, 59% and 73% had a family history of CVD. Out of 124 patients, only 13 had genetic testing through their clinical care, all of which occurred post-transplantation. 5/13 of these patients had a P/LP variant. Conclusions: This retrospective study showed a significant yield of genetic testing in HT patients. Notably, the overall prevalence of P/LP variants was nearly identical between NICM and ICM patients, with a higher rate of CM-related variants in the NICM group. We suggest that a genotype-first approach of screening all HT patients for genetic mutations enables earlier identification of actionable variants in HT probands and their family members than the current phenotype-guided approach.

Optical Genome Mapping Allows Detection and Characterization of Cytogenetically Cryptic Oncogenic Fusions in Pediatric Acute Myeloid Leukemia

Background: Abnormal gene fusions are predominant oncogenic drivers in pediatric acute myeloid leukemia (AML) and are important diagnostic and prognostic markers. However, several oncogenic fusions specific for or enriched in pediatric AML (like CBFA2T3::GLIS2, NUP98::NSD1, ETV6::MNX1 and others) are not detectable by conventional cytogenetic analysis (cytogenetically cryptic) and may not be included in fluorescence in situ hybridization (FISH) or molecular fusion panels designed for adult patients. Optical genome mapping (OGM) is a powerful new method for genome-wide, high-resolution detection of copy number abnormalities and balanced chromosome rearrangements. This study determined the frequency of cryptic oncogenic fusions in an institutional cohort of pediatric AML cases and evaluated OGM as a method for their detection and characterization. Methods: Retrospective review of genetic testing results was performed for 93 consecutive de novo or relapsed pediatric AML cases tested at the Children's Hospital Los Angeles (CHLA) Center for Personalized Medicine between March 2016 and July 2023. Genetic testing was performed as part of clinical care following standard procedures and consisted of karyotype analysis, FISH testing, chromosomal microarray (CMA) analysis, CHLA custom sequencing panel (OncoKids®) (June 2017 onwards) and RNA-Seq fusion assay (March 2022 onwards). Cases with normal or inconclusive karyotype in which an oncogenic fusion was detected by another clinical assay were selected for OGM testing. High molecular weight DNA from peripheral blood or bone marrow samples was labeled, processed and imaged in a Saphyr System and analyzed in the Bionano Access software following the manufacturer's recommendations (BionanoGenomics, San Diego CA). Results: Out of 93 pediatric AML cases included in the study, a gene fusion was identified as the primary oncogenic driver in 54 (58%) and a DNA sequence variant in 11 (12%). In 28 cases (30%), the primary genetic abnormality remained undetermined after comprehensive genetic testing. In 17/54 (31%) fusion-driven cases [17/93 (18%) overall cases], the oncogenic fusion remained undetected by karyotype analysis (cryptic). OGM was completed in 13/17 fusion positive cases with non-informative karyotype; it could not be performed in 4 cases due to lack of samples (n=2) or poor DNA quality (n=2), and is still in progress for a subset of 28 unknown cases with available material. OGM analysis successfully revealed all cryptic fusions previously detected by FISH, CMA, OncoKids® and/or RNA-Seq, including NUP98::NSD1 (n=3), KMT2A::MLLT10 (n=3), KMT2A::MLLT3 (n=2)and one case each of CBFA2T3::GLIS2, NUP98::KDM5A, DEK::NUP214, MYB::GATA1 and ETV6::MNX1. Chromosomal mechanism and structure of cryptic fusions were resolved by OGM and included: intrinsically cryptic fusions due to chromosome location of partner genes ( NUP98::NSD1, n=4; CBFA2T3::GLIS2, NUP98::KDM5A and ETV6::MNX1, n=1 each); complex rearrangements due to incompatible gene orientation ( KMT2A::MLLT10 n=2; MYB::GATA1, n=1); three-way rearrangements involving an additional chromosome ( KMT2A::MLLT3 n=2) and small insertions ( KMT2A::MLLT10 and DEK::NUP214, n=1 each). OGM also matched the performance of chromosomal microarray (CMA) analysis in detection of copy number variants. Conclusions: We confirm the significant contribution of cryptic chromosome rearrangements to pathogenesis of pediatric AML, and highlight the importance of tailored testing approaches that effectively detect highly heterogeneous fusion drivers. Our preliminary results show potential of OGM to identify clinically significant cryptic fusions in pediatric AML, and to thus markedly increase diagnostic yield compared to karyotype analysis. As a single assay that detects abnormalities currently interrogated by conventional cytogenetics, FISH and CMA, OGM may allow streamlined and more cost-effective genetic evaluation for pediatric AML.

Human-genome single nucleotide polymorphisms affecting transcription factor binding and their role in pathogenesis.

Single nucleotide polymorphisms (SNPs) are the most common type of variation in the human genome. The vast majority of SNPs identified in the human genome do not have any effect on the phenotype; however, some can lead to changes in the function of a gene or the level of its expression. Most SNPs associated with certain traits or pathologies are mapped to regulatory regions of the genome and affect gene expression by changing transcription factor binding sites. In recent decades, substantial effort has been invested in searching for such regulatory SNPs (rSNPs) and understanding the mechanisms by which they lead to phenotypic differences, primarily to individual differences in susceptibility to diseases and in sensitivity to drugs. The development of the NGS (next-generation sequencing) technology has contributed not only to the identification of a huge number of SNPs and to the search for their association (genome-wide association studies, GWASs) with certain diseases or phenotypic manifestations, but also to the development of more productive approaches to their functional annotation. It should be noted that the presence of an association does not allow one to identify a functional, truly disease-associated DNA sequence variant among multiple marker SNPs that are detected due to linkage disequilibrium. Moreover, determination of associations of genetic variants with a disease does not provide information about the functionality of these variants, which is necessary to elucidate the molecular mechanisms of the development of pathology and to design effective methods for its treatment and prevention. In this regard, the functional analysis of SNPs annotated in the GWAS catalog, both at the genome-wide level and at the level of individual SNPs, became especially relevant in recent years. A genome-wide search for potential rSNPs is possible without any prior knowledge of their association with a trait. Thus, mapping expression quantitative trait loci (eQTLs) makes it possible to identify an SNP for which - among transcriptomes of homozygotes and heterozygotes for its various alleles - there are differences in the expression level of certain genes, which can be located at various distances from the SNP. To predict rSNPs, approaches based on searches for allele-specific events in RNA-seq, ChIP-seq, DNase-seq, ATAC-seq, MPRA, and other data are also used. Nonetheless, for a more complete functional annotation of such rSNPs, it is necessary to establish their association with a trait, in particular, with a predisposition to a certain pathology or sensitivity to drugs. Thus, approaches to finding SNPs important for the development of a trait can be categorized into two groups: (1) starting from data on an association of SNPs with a certain trait, (2) starting from the determination of allele-specific changes at the molecular level (in a transcriptome or regulome). Only comprehensive use of strategically different approaches can considerably enrich our knowledge about the role of genetic determinants in the molecular mechanisms of trait formation, including predisposition to multifactorial diseases.

Discovery of a new species of dwarf frog (Anura: Ceratobatrachidae: Alcalus) extends the northwestern distributional limits of the genus to Northeast India

We describe a new species of the genus Alcalus from the northeast Indian state of Arunachal Pradesh based on molecular, morphological, and osteological characters. The new species differs from its congeners based on a combination of morphological characters including snout-vent length (27–28 mm in males; 29.9–36.2 mm in females), disc on fingers and toes with horizontal/transverse groove on the dorsal surface, dorsal skin wrinkled, and a pair of faint dorsolateral stripes on back. The new species also differs from its congeners by a DNA sequence divergence of 7.6–25.4% in the mitochondrial gene fragment 12S–tVal–16S rRNA (1533 base pairs). We include a detailed osteological description of the new species and compare it with the type of this genus. This is the first record of this genus from India, which was recently also reported from Myanmar and Western China. Discovery of a new species from northeast India indicates the need for a systematic study to uncover the hidden diversity of the Indo-Burma biodiversity hotspot. http://zoobank.org/urn:lsid:zoobank.org:pub:FB75F850-2AD9-4643-97CE-7F3F1D58E3F8 http://zoobank.org/urn:lsid:zoobank.org:act:6104F7A5-7E5E-42A7-90A1-810C394CFB3E

SHIP: identifying antimicrobial resistance gene transfer between plasmids.

Plasmids are carriers for antimicrobial resistance (AMR) genes and can exchange genetic material with other structures, contributing to the spread of AMR. There is no reliable approach to identify the transfer of AMR genes across plasmids. This is mainly due to the absence of a method to assess the phylogenetic distance of plasmids, as they show large DNA sequence variability. Identifying and quantifying such transfer can provide novel insight into the role of small mobile elements and resistant plasmid regions in the spread of AMR. We developed SHIP, a novel method to quantify plasmid similarity based on the dynamics of plasmid evolution. This allowed us to find conserved fragments containing AMR genes in structurally different and phylogenetically distant plasmids, which is evidence for lateral transfer. Our results show that regions carrying AMR genes are highly mobilizable between plasmids through transposons, integrons, and recombination events, and contribute to the spread of AMR. Identified transferred fragments include a multi-resistant complex class 1 integron in Escherichia coli and Klebsiella pneumoniae, and a region encoding tetracycline resistance transferred through recombination in Enterococcus faecalis. The code developed in this work is available at https://github.com/AbeelLab/plasmidHGT.

Molecular identification of Eimeria spp. and Eimeria bovis in water buffaloes, Iraq

Eimeria is a protozoan parasite of many wild and domestic animals including buffaloes resulting in a widespread disease known as coccidiosis that may impact production, well fare and health status. This study was designed to identify the prevalence of Eimeria spp. and E. bovis in buffaloes using conventional molecular technique. An overall 281 buffaloes of different sexes and ages of many rural areas in Wasit province were subjected during November (2022) to February (2023) to direct collect of fecal samples from the rectum. After molecular examination of all fecal samples by polymerase chain reaction (PCR), the results showed that 25.98 and 35.62% buffaloes were positive to Eimeria spp. and E. bovis, respectively. Furthermore, significant prevalence of Eimeria spp. being higher in  1 year than older ones and Al-Kut than other study region, but not between females and males; while, E. bovis was more prevalent in  1 year, Al-Kut and Al-Hay, and females. Additionally, values of odds ratio and relative risk were elevated significantly in  1 year female buffaloes of Al-Kut region. From our point of view, this represents the first molecular study identifies E. bovis in buffaloes from Iraq. In conclusion, molecular based-PCR revealed a high efficacy in identification of E. bovis, and can be used in epidemiological investigations of coccidiosis in entire country. However, we suggest that the DNA sequence variation in ITS1 region of different Eimeria species should be conducted to view genetic mutations as well as genetic association with other worldwide strains. Also, extensive investigation is necessary to bridge the knowledge gap and providing for diagnosis this parasite in buffaloes as well as in other field animals. Keywords: Coccidiosis, PCR, Bubalus bubalis, calf, wasit province. Iraq

Analysis of genetic polymorphism in genes encoding cathelicidins from Vietnam indigenous yellow cattle breeds

Cathelicidins include antimicrobial peptides (AMPs) and are involved in the innate immune defense against infections in mammals. Polymorphisms in the DNA sequence of cathelicidin genes could be relevant to inherited variations of host innate immunity, adaptation, and pathogen resistance. This study aims to investigate the sequence polymorphism of cathelicidin genes including CATHL2 and CATHL4 from local indigenous yellow cattle breeds of Vietnam. Genomic DNA samples were extracted from 52 individuals collected from different cattle populations in Vietnam including Ha Giang, Thanh Hoa, Nghe An and Phu Yen. The CATHL2 and CATHL4 genes were amplified by PCR, following sequencing for identification of the single nucleotide polymorphisms (SNPs) and/or insertion-deletion (indel) DNA sequence variations. The copy number variations (CNVs) of the CATHL4 gene were determined by cloning, single strand conformation polymorphism (SSCP) and real-time PCR. The comparative analysis results showed that there are 13 SNPs detected in all sequences of CATHL2 gene including 9 SNPs in intron 2 and intron 3, and 4 missense substitutions in exon 1, 2, and 3. These SNPs do not affect the predicted tertiary structure of Bac5 encoded by this gene. For CATHL4, the results revealed 15 SNPs, 3 indels and 1 repeat variation as motif (TG)n(G)n/(AC)n(C)n. Among these variations, the deletion 46delC in exon 1 of CATHL4 was detected in a sample of the Ha Giang breed causing a truncated polypeptide as predicted. The average copy number of CATHL4 of Vietnam indigenous cattle breeds using GADPH as a reference gene showed in range from 2.53 to 2.89 copies.

Short-read aligner performance in germline variant identification.

Read alignment is an essential first step in the characterization of DNA sequence variation. The accuracy of variant calling results depends not only on the quality of read alignment and variant calling software but also on the interaction between these complex software tools. In this review, we evaluate short-read aligner performance with the goal of optimizing germline variant calling accuracy. We examine the performance of three general-purpose short-read aligners - BWA-MEM, Bowtie 2, and Arioc - in conjunction with three germline variant callers: DeepVariant, FreeBayes, and GATK HaplotypeCaller. We discuss the behavior of the read aligners with regard to the data elements on which the variant callers rely, and illustrate how the runtime configurations of these software tools combine to affect variant calling performance. The quick brown fox jumps over the lazy dog. Supplementary information is available at Bioinformatics online.