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At least 37 records · Page 2Linked to original sources
PubMed2001

DACH: genomic characterization, evaluation as a candidate for postaxial polydactyly type A2, and developmental expression pattern of the mouse homologue.

The gene DACH is a human homologue of Drosophila melanogaster dachshund (dac), which encodes a nuclear factor essential for determining cell fates in the eye, leg, and nervous system of the fly. To investigate possible connections between DACH and inherited developmental disorders, we have characterized the human DACH genomic structure and investigated the tissue and cellular distribution of the mouse DACH1 protein during development. DACH spans 400 kb and is encoded by 12 exons. The predominant DACH transcript is 5.2 kb and encodes a 706-amino-acid protein with an observed molecular weight of 97 kDa.DACH mRNA was detected in multiple adult human tissues including kidney and heart. The mouse DACH1 protein was immunolocalized to specific cell types within the developing kidneys, eyes, cochleae, and limb buds. Data suggest genetic linkage of the limb bud patterning defect postaxial polydactyly type A (designated PAP-A2, MIM 602085) to a 28-cM interval on chromosome 13 that includes DACH. However, mutation analysis of DACH in this PAP-A2 pedigree revealed no sequence differences in the coding region, splice sites, or proximal promoter region. The data presented will allow for the analysis of DACH as a candidate for other developmental disorders affecting the limbs, kidneys, eyes, ears, and other sites of DACH expression.

Alternative Splicing↗
PubMed2000

Quantitative evaluation of genomic instability as a possible predictor for development of hepatocellular carcinoma: comparison of loss of heterozygosity and replication error.

Both loss of heterozygosity (LOH) and replication error (RER) are considered to be phenotypes of genomic instability. To unveil the role of the genomic instability in hepatocarcinogenesis, frequencies of LOH and RER were simultaneously determined in 15 hepatocellular carcinomas (HCCs), surrounding nontumorous liver tissues (SL), and 13 liver tissues with chronic viral hepatitis void of cancer (NC) by referencing peripheral blood leukocytes (PBLs) from the corresponding donor using 18 microsatellite markers spread throughout the genome. LOH was significantly frequent in HCC compared with that in SL or NC (P =.005, P =.0003, respectively) and observed preferentially at particular microsatellite loci, D1S204, D2S123, D8S1106, D9S266, D16S748, and D19S601. Although the higher prevalence of RER was also significant in HCC compared with that in NC (P =.03), in most cases the errors were detected at very low frequencies and random loci. Both LOH and RER tended to appear more prevalently in SL than in NC. The occurrence rate of LOH was higher in the tissues associated with hepatitis B virus (HBV) than with hepatitis C virus (HCV) infection especially in HCC (P =.03). When referencing SL instead of PBLs, the prevalence of LOH and RER in HCC significantly decreased (P =.02 and P =.03, respectively). These results suggest that LOH is closely associated with multistep hepatocarcinogenesis especially under HBV infection, but RER is imperceptibly associated. The quantitative evaluation of the frequency of LOH by referencing PBLs may be a useful predictor for HCC development in chronic liver diseases.

Blood Cells↗
PubMed2002

Chromosomal analysis of hepatic adenoma and focal nodular hyperplasia by comparative genomic hybridization.

Hepatic adenoma (HA) and focal nodular hyperplasia (FNH) are two common non-malignant tumors of the liver. Genomic analysis on these benign lesions may shed light on the genetic mechanism underlying liver carcinogenesis. We used comparative genomic hybridization (CGH) to evaluate genomic changes in eight cases of HA and six cases of FNH, obtained by surgical procedures; the resulting chromosomal aberration profiles were analyzed together with their pathological and clinical manifestations. We found consistent chromosomal lesions associated with both non-malignant hepatic tumors. The overall genomic abnormalities in HA and FNH were much less obvious than those in hepatocellular carcinoma (HCC). Among these limited changes, frequent gains were located on chromosomal arms 1q (50%), 17q (50%), 1p (38%), and 11q (38%) in HA, and on 11q (50%), 9q (33%), 17q (33%), and 22q (33%) in FNH. Gains outnumbered losses, and HA contained more CGH abnormalities than did FNH. Interestingly, CGH alteration hotspots found in HA, but not in FNH, appeared largely to coincide with common genomic lesions of cancerous HCC, suggesting an interesting relationship along the tumorigenesis pathway of HA and HCC.

Adenoma↗
PubMed2004

Evaluation of genomic changes in a large series of malignant ovarian germ cell tumors--relation to clinicopathologic variables.

Malignant ovarian germ cell tumors (mOGCT) affect women in their reproductive years, making fertility-saving treatment important. A reliable prediction of the clinical behavior is essential for an optimal therapeutic approach. The genetic changes and molecular mechanisms underlying these rare tumors remain poorly understood. To address these issues, we performed DNA ploidy analysis by high-resolution image cytometry in a series of 47 mOGCT and correlated the findings with the DNA copy number changes detected by comparative genomic hybridization (CGH) and clinical outcome. Of 47 tumors, 15 were diploid, 14 were tetraploid, 2 were polyploid, and 13 were aneuploid. All the immature teratomas were diploid, in contrast to the dysgerminomas and endodermal sinus tumors. The International Federation of Gynecology and Obstetrics (FIGO) staging, residual tumors after surgery, and DNA ploidy distribution were significant, independent prognostic factors in survival analysis. The study revealed that the number of DNA copy number aberrations was increased in tetraploid and aneuploid tumors as compared to diploid tumors. Furthermore, a high percentage of aneuploid nuclei in a sample were associated with a complex CGH profile of the tumor in question. The present study confirms that DNA aneuploidy assessment by image analysis may be linked to genetic instability, which is detected as genetic aberrations by CGH. DNA ploidy gives significant prognostic information in addition to the clinical stage in mOGCT with FIGO stage II-IV.

Adolescent↗
PubMed2005

Evaluating whole genome amplification via multiply-primed rolling circle amplification for SNP genotyping of samples with low DNA yield.

The amount of available DNA is often a limiting factor in pursuing genetic analyses of large-scale population cohorts. An association between higher DNA yield from blood and several phenotypes associated with inflammatory states has recently been demonstrated, suggesting that exclusion of samples with very low DNA yield may lead to biased results in statistical analyses. Whole genome amplification (WGA) could present a solution to the DNA concentration-dependent sample selection. The aim was to thoroughly assess WGA for samples with low DNA yield, using the multiply-primed rolling circle amplification method. Fifty-nine samples were selected with the lowest DNA yield (less than 7.5 microg) among 799 samples obtained for one population cohort. The genotypes obtained from two replicate WGA samples and the original genomic DNA were compared by typing 24 single nucleotide polymorphisms (SNPs). Multiple genotype discrepancies were identified for 13 of the 59 samples. The largest portion of discrepancies was due to allele dropout in heterozygous genotypes in WGA samples. Pooling the WGA DNA replicates prior to genotyping markedly improved genotyping reproducibility for the samples, with only 7 discrepancies identified in 4 samples. The nature of discrepancies was mostly homozygote genotypes in the genomic DNA and heterozygote genotypes in the WGA sample, suggesting possible allele dropout in the genomic DNA sample due to very low amounts of DNA template. Thus, WGA is applicable for low DNA yield samples, especially if using pooled WGA samples. A higher rate of genotyping errors requires that increased attention be paid to genotyping quality control, and caution when interpreting results.

DNA↗
PubMed1991

Amplification by the polymerase chain reaction of hypervariable regions of the human genome for evaluation of chimerism after bone marrow transplantation.

We combined the polymerase chain reaction (PCR) with oligonucleotide hybridization as a novel and sensitive technique to evaluate posttransplant chimerism. Specific oligonucleotides for hybridization were synthesized homologous to tandemly repetitive core sequences of regions with a variable number of tandem repeats (VNTRs). Polymorphisms at such loci result from allelic differences in the number of repeats. Primers flanking the repeat region of each of the corresponding VNTRs were used for amplification. Recipient and donor pretransplant DNA and recipient posttransplant DNA were amplified. The resultant fragments were analyzed after gel electrophoresis either by hybridization in-gel or after Southern transfer. To confirm our findings, we also performed standard assays of restriction fragment length polymorphisms (RFLPs). Evaluation of 13 selected cases indicated mixed chimerism (4), complete chimerism (5), recurrence of leukemia (2), and endogenous repopulation of hematopoiesis (2) after marrow transplantation. Sensitivity of the method was determined by mixing various proportions of recipient and donor DNA; the limit of detection of the minor component in a mixture was 0.1%. PCR data correlated with RFLP data in all cases except two in which PCR proved more sensitive than RFLP. PCR amplification of VNTRs combined with oligonucleotide hybridization is a novel technique for documenting posttransplant chimerism and has advantages over RFLP analysis: high sensitivity, use of small amounts of DNA (250 ng), ease of preparation of DNA, elimination of need for restriction enzymes, and the ability to complete studies in 2 days.

Base Sequence↗
PubMed1994

[Summary and evaluation of genome and antibody diagnosis in hepatitis C virus infection].

Hepatitis C virus (HCV) infection can be diagnosed by antibody assay systems using recombinant antigens since the HCV genome has been identified. It is still impossible to detect viral antigens associated with HCV. Therefore, the polymerase chain reaction (PCR) has been widely used in practical laboratory examinations. Because HCV is an RNA virus and the reverse transcription process is required prior to the PCR reaction, the process of HCV RNA detection has a risk of contamination and the detection rate may differ with the PCR condition. There are several genome diagnostic methods for HCV infection; that is, genome detection by nested PCR, HCV subtyping using mixed primer, quantitation of HCV genome using competitive PCR, Quant-Amp and branched DNA probe. To clarify what factors are responsible, the efficacy of interferon therapy against chronic hepatitis C was examined. The normalization rate of serum ALT level and clearance rate of HCV RNA in serum at six months after the end of the treatment were correlated to the titer of HCV RNA genome and the HCV subtype. The patients with HCV RNA titers of less than 10(4) copies/50 microliters and with subtype group III showed a high response to interferon administration. On the other hand, the results of quantitation of the HCV core antibody titer were closely associated with the presence of HCV RNA using core protein with the recombinant vaccinia expression system or recombinant E. coli system (JCC-2). Especially, in the group of high responders to interferon treatment, the antibody titer against core protein was apparently decreased after the end of interferon therapy.(ABSTRACT TRUNCATED AT 250 WORDS)

Genome, Viral↗
PubMed2006

[A complex approach to evaluation of human genome instability].

In this study, evaluation of genome instability in individuals exposed to chemical compounds included detection of the genetic polymorphism of some xenobiotic metabolic enzymes (CYP1A1, CYP1E1, PON1, GSTM1, GSTT1), as well as measurement of oxidative state chemiluminescent variables and the level of cytogenetic damage. According to the study, the level of chromosomal aberrations in peripheral blood lymphocytes shows a strong correlation with PON54 left allele and GSTM1 null genotype, and can be described by the polynomial function of blood plasma luminol-dependent chemiluminescence. The frequencies of micronuclei in buccal epithelium displayed a weak association with GSTT1 null genotype.

Genome, Human↗
PubMed2005

Genomic and non-genomic effects of different glucocorticoids on mouse thymocyte apoptosis.

Glucocorticoids, widely used therapeutic agents for several pathologies, act upon diverse cells and tissues, including the lympho-haemopoietic system. Glucocorticoid-mediated apoptosis has been described as one of the mechanisms underlying their pharmacological and physiological effects. Glucocorticoids induce apoptosis in thymocytes through genomic and non-genomic signals. We tested thymocyte apoptosis rates as induced by a panel of glucocorticoids. Using four glucocorticoids that are widely adopted in clinical practice we compared their induction of thymocyte apoptosis and activation of non-genomic and genomic signals, including phosphatidylinositol-specific phospholipase C (PI-PLC), caspase-8, -9 and -3, and Glucocorticoid-Induced Leucine Zipper (GILZ). GILZ is a protein that is rapidly induced by glucocorticoids treatment and involved in apoptosis modulation. Results indicate different glucocorticoids have different apoptotic activity which is related to their ability to induce both genomic, evaluated as caspases activation and GILZ expression, and non-genomic effects, evaluated as PI-PLC phosphorylation.

Animals↗
PubMed2026

Enhancing CRISPR-Cas12a base editing in plants with LbCas12a variants and introns.

Cytosine base editors (CBEs) and adenine base editors (ABEs) are powerful tools for precise genome editing in plants. Conventionally, such base editors are built upon the CRISPR-Cas9 systems where Cas9 nickases are used. To expand the base editing scope and minimize off-target effects, base editors derived from the CRISPR-Cas12a systems are desired. However, the use of deactivated Cas12a (dCas12a) in such base editors constrains the editing activity, preventing the wide use of Cas12a base editors for plant research and trait development. In this study, we demonstrate the use of an ABE based on the efficient LbCas12a-RRV variant to introduce herbicide-resistant mutations in OsACCase in rice. To improve Cas12a CBEs and ABEs, we inserted introns into the coding sequence of dLbCas12a-RRV. This intron-containing Cas12a-CBE shows substantial improvement in editing efficiency in rice, compared to the intron-less counterparts. By contrast, the improvement of ABE with the intron-containing dLbCas12a-RRV is very limited, partly due to the already high baseline editing efficiency of the intron-less dLbCas12a-RRV ABE. Testing of these base editors in poplar shows elevated C-to-T base editing by dLbCas12a-RRV-intron-CBE. For A-to-G editing, ABEs built upon dLbCas12a-RV and dLbCas12a-RRV variants showed significant improvement over ABEs derived from wild-type LbCas12a and the ttLbCas12a variant. The addition of introns to dLbCas12a-RRV does not further improve the base editing efficiency. With whole genome sequencing in rice, we evaluated genome editing specificities with these improved Cas12a base editors. Our analyses show that both intron-containing Cas12a CBE and ABE barely introduce guide RNA-dependent off-target mutations. However, they can generate guide RNA-independent off-target mutations, which are likely attributed to the high enzymatic activities of the deaminases. Collectively, our study demonstrates the successful use of a Cas12a base editor for trait development and reports improved Cas12a CBEs and ABEs for precise base editing in plants.

Oryza↗
PubMed2023

Utilizing evolutionary conservation to detect deleterious mutations and improve genomic prediction in cassava.

INTRODUCTION: Cassava (Manihot esculenta) is an annual root crop which provides the major source of calories for over half a billion people around the world. Since its domestication ~10,000 years ago, cassava has been largely clonally propagated through stem cuttings. Minimal sexual recombination has led to an accumulation of deleterious mutations made evident by heavy inbreeding depression. METHODS: To locate and characterize these deleterious mutations, and to measure selection pressure across the cassava genome, we aligned 52 related Euphorbiaceae and other related species representing millions of years of evolution. With single base-pair resolution of genetic conservation, we used protein structure models, amino acid impact, and evolutionary conservation across the Euphorbiaceae to estimate evolutionary constraint. With known deleterious mutations, we aimed to improve genomic evaluations of plant performance through genomic prediction. We first tested this hypothesis through simulation utilizing multi-kernel GBLUP to predict simulated phenotypes across separate populations of cassava. RESULTS: Simulations showed a sizable increase of prediction accuracy when incorporating functional variants in the model when the trait was determined by<100 quantitative trait loci (QTL). Utilizing deleterious mutations and functional weights informed through evolutionary conservation, we saw improvements in genomic prediction accuracy that were dependent on trait and prediction. CONCLUSION: We showed the potential for using evolutionary information to track functional variation across the genome, in order to improve whole genome trait prediction. We anticipate that continued work to improve genotype accuracy and deleterious mutation assessment will lead to improved genomic assessments of cassava clones.

cassava (Manihot esculenta)↗
PubMed2026

Sparse phenotyping for wheat grain yield enabled by multiomics prediction.

Grain yield is a central target in wheat breeding, yet accurately predicting it remains challenging because it depends on many genes and responds strongly to environmental variation. Genomic selection (GS) has improved breeding efficiency by enabling genome-based prediction of genetic merit, but predictability (PA) for grain yield is often limited under stress environments. At the same time, advances in high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) provide phenomic data that capture environment-responsive plant performance and may complement genomic information. In this study, we evaluated genomic and phenomic models for predicting grain yield in elite bread wheat lines across irrigated, drought, and heat-stress environments. Using a sparse phenotyping framework, we compared parametric and non-parametric models. PA was evaluated within environments and under cross-environment sparse phenotyping scenarios. Genomic models provided a stable baseline and enabled effective information sharing across environments when phenotypic data were incomplete. Phenomics-only models captured environment-specific plant responses but were more sensitive to environmental context. Multiomics models that integrated genomic and phenomic information consistently achieved the highest PA, with the largest gains observed under stress conditions. Overall, our results demonstrate that integrating genomics and UAV-based phenomics within sparse phenotyping designs offers a practical and scalable approach to improve grain yield prediction in wheat.

Triticum↗
PubMed1994

Genome scanning detects genetic alterations in human ovarian carcinoma.

Genome scanning, originally used to detect mouse mutations, is a technique which can rapidly identify differences between genomic DNA samples. The procedure is essentially a high resolution Southern analysis using a probe that hybridizes to a medium copy number (1000-2000 copies per haploid genome) repetitive element naturally dispersed throughout the genome. This technique detects genetic changes (primarily large scale genetic changes, e.g., amplifications and deletions) as differences in hybridization band intensity. The use of a probe derived from an endogenous human retroviral-like repetitive sequence, the RTVL-H element, has made genome scanning in humans feasible. In this report, the genome scanning technique was used to evaluate genomic DNA extracted from 14 frozen ovarian tumors. These included 8 high grade serous cystadenocarcinomas, 2 endometrioid carcinomas, one malignant mixed mullerian tumor, 2 Krukenberg tumors, and one tumor where histological classification was unavailable. Band amplifications were identified in 11 cases, with the most prominent amplifications observed in the high grade serous cystadenocarcinomas. In some of the cases, the amplifications involved bands of identical molecular size suggesting that similar underlying changes occurred in different tumors and are potentially associated with specific histological tumor types or clinical behavior. Band deletions were also observed in one endometrioid tumor where blood leukocyte genomic DNA was available from the same patient, allowing a direct comparison.

DNA Probes↗
PubMed2005

The future of animal models of invasive aspergillosis.

The diagnosis of invasive aspergillosis remains very difficult, coupled with limited treatment options. Animal models have been utilized to evaluate both the diagnosis and treatment of infection and to assess the pathogenicity and virulence of the organism. However, animal models have not been standardized and have been used in only a limited fashion for genomic evaluation in this disease. Extensive efforts are underway to expand significantly the Aspergillus genomic information. Thus, the standardization of animal models of invasive aspergillosis is critical to create a unified platform to enhance evaluation of newer genomic information and allow assessment of pathogenicity and virulence factors. Proposed models, supported by a recently awarded National Institutes of Health/National Institute of Allergy and Infectious Diseases contract, will be developed in close interaction with the extended Aspergillus community (including academia and industry) to answer key questions in this disease. The goal of this work is to provide the framework to evaluate genomic targets in animal models in order to improve the diagnosis and treatment of invasive aspergillosis that will ultimately result in improved outcomes of patients with this frequently fatal infection.

Animals↗
PubMed2006

Finding function: evaluation methods for functional genomic data.

BACKGROUND: Accurate evaluation of the quality of genomic or proteomic data and computational methods is vital to our ability to use them for formulating novel biological hypotheses and directing further experiments. There is currently no standard approach to evaluation in functional genomics. Our analysis of existing approaches shows that they are inconsistent and contain substantial functional biases that render the resulting evaluations misleading both quantitatively and qualitatively. These problems make it essentially impossible to compare computational methods or large-scale experimental datasets and also result in conclusions that generalize poorly in most biological applications. RESULTS: We reveal issues with current evaluation methods here and suggest new approaches to evaluation that facilitate accurate and representative characterization of genomic methods and data. Specifically, we describe a functional genomics gold standard based on curation by expert biologists and demonstrate its use as an effective means of evaluation of genomic approaches. Our evaluation framework and gold standard are freely available to the community through our website. CONCLUSION: Proper methods for evaluating genomic data and computational approaches will determine how much we, as a community, are able to learn from the wealth of available data. We propose one possible solution to this problem here but emphasize that this topic warrants broader community discussion.

Algorithms↗
PubMed2026

An economic evaluation of functional genomic testing for individuals with undiagnosed rare disorders.

PURPOSE: Functional genomics (FG) approaches, such as RNA-seq and proteomics, offer a complementary diagnostic modality for individuals whose cases remain unsolved after genomic sequencing. This study evaluates the cost-effectiveness and cost-benefit of FG for individuals with suspected monogenic disorders relative to manual reanalysis of genomic data at 18 months. METHODS: A decision tree model compared the costs and outcomes of FG and 18-month reanalysis using data from two Australian Undiagnosed Disease Programs. Deterministic and probability sensitivity analysis were performed. RESULTS: With a diagnostic yield of 13%, FG enabled 4 additional diagnoses per 100 individuals tested at an additional cost of $390 (US $240), resulting in an incremental cost-effectiveness ratio of $8,550 ($5,313) and an 85% probability of being cost-effective. CONCLUSION: Functional genomics enables timely diagnosis for individuals with suspected monogenic disorders by evaluating the functional impact of variants of uncertain significance, offering an advantage over reanalyzing genomic data at 18 months. Integration into the Australian healthcare system, supported by collaborative networks and secure data-sharing infrastructure, coupled with addressing barriers to accessing funded genomic testing, could lead to an annual net benefit of up to $1.1 million ($0.7 M).

Functional genomics↗
PubMed1979

A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes.

A new approach for evaluating homologous sequences among related DNAs is presented. Conventional filter hybridization techniques are employed at 35 degrees C in a range of formamide concentrations in order to perform annealings at effective temperatures as low as Tm -50 degrees C which permits the detection of regions of homology with as much as 33% base mismatch. Under such nonstringent conditions, high levels of specific annealing can be obtained at plateau levels. In combination with the Southern "blotting" technique (1975), this approach can be used to perform biochemical heteroduplex melting experiments. The homology among the genomes of the murine polyoma virus (Py), the simian virus 40 (SV40), and the human papovavirus BK was evaluated using this new methodology.

DNA, Viral↗