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At least 55 records · Page 3Linked to original sources
PubMed2025

Clinical utility of comprehensive genomic profiling test for colorectal cancer: a single institution prospective observational study.

PURPOSE: Next-generation sequencing (NGS) has revolutionized cancer treatment by enabling comprehensive cancer genomic profiling (CGP) to guide genotype-directed therapies. While several prospective trials have demonstrated varying outcomes with CGP in patients with advanced solid tumors, its clinical utility in colorectal cancer (CRC) remains to be evaluated. METHODS: We conducted a prospective observational study of CGP in our hospital between September 2019 and March 2024. Overall survival (OS) of the patients who received CGP-based therapy and those did not was compared, and genomic variables associated with OS were evaluated. RESULTS: A total of 100 patients with CRC underwent CGP using four platforms. The median patient age was 67 years, and most had a good performance status. The most frequent genomic alterations were TP53 (82%), APC (82%), and KRAS (55%). Actionable mutations such as ERBB2 amplification and BRAF V600E were identified in some patients, and 9% received CGP-based therapy, including immune checkpoint inhibitors for tumor mutational burden-high or microsatellite instability-high tumors. Patients receiving CGP-based therapy had longer OS from expert panel discussion (16.0 vs. 10.8 months) compared to those who did not. Alterations in TP53, SMAD4, and NF1 were associated with worse OS. Interestingly, PTEN mutations were linked to improved survival. TP53 alterations were more common in left-sided CRC. CONCLUSION: Although some patients with CRC received CGP-guided therapy, a statistically significant survival benefit was not observed. However, TP53 and SMAD4 mutations were identified as negative prognostic markers, indicating their potential as targets for future drug development.

Humans↗
PubMed2003

Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria.

We address the problem of clustering the whole protein content of genomes into three different categories-globular, all-alpha, and all-beta membrane proteins-with the aim of fishing new membrane proteins in the pool of nonannotated proteins (twilight zone). The focus is then mainly on outer membrane proteins. This is performed by using an integrated suite of programs (Hunter) specifically developed for predicting the occurrence of signal peptides in proteins of Gram-negative bacteria and the topography of all-alpha and all-beta membrane proteins. Hunter is tested on the well and partially annotated proteins (2160 and 760, respectively) of Escherichia coli K 12 scoring as high as 95.6% in the correct assignment of each chain to the category. Of the remaining 1253 nonannotated sequences, 1099 are predicted globular, 136 are all-alpha, and 18 are all-beta membrane proteins. In Escherichia coli 0157:H7 we filtered 1901 nonannotated proteins. Our analysis classifies 1564 globular chains, 327 inner membrane proteins, and 10 outer membrane proteins. With Hunter, new membrane proteins are added to the list of putative membrane proteins of Gram-negative bacteria. The content of outer membrane proteins per genome (nine are analyzed) ranges from 1.5% to 2.4%, and it is one order of magnitude lower than that of inner membrane proteins. The finding is particularly relevant when it is considered that this is the first large-scale analysis based on validated tools that can predict the content of outer membrane proteins in a genome and can allow cross-comparison of the same protein type between different species.

Bacterial Outer Membrane Proteins↗
PubMed2006

Copy number variation in regions flanked (or unflanked) by duplicons among patients with developmental delay and/or congenital malformations; detection of reciprocal and partial Williams-Beuren duplications.

Duplicons, that is, DNA sequences with minimum length 10 kb and a high sequence similarity, are known to cause unequal homologous recombination, leading to deletions and the reciprocal duplications. In this study, we designed a Multiplex Amplifiable Probe Hybridisation (MAPH) assay containing 63 exon-specific single-copy sequences from within a selection of the 169 regions flanked by duplicons that were identified, at a first pass, in 2001. Subsequently, we determined the frequency of chromosomal rearrangements among patients with developmental delay (DD) and/or congenital malformations (CM). In addition, we tried to identify new regions involved in DD/CM using the same assay. In 105 patients, six imbalances (5.8%) were detected and verified. Three of these were located in microdeletion-related regions, two alterations were polymorphic duplications and the effect of the last alteration is currently unknown. The same study population was tested for rearrangements in regions with no known duplicons nearby, using a set of probes derived from 58 function-selected genes. The latter screening revealed two alterations. As expected, the alteration frequency per unit of DNA is much higher in regions flanked by duplicons (fraction of the genome tested: 5.2%) compared to regions without known duplicons nearby (fraction of the genome tested: 24.5-90.2%). We were able to detect three novel rearrangements, including the previously undescribed reciprocal duplication of the Williams Beuren critical region, a subduplicon alteration within this region and a duplication on chromosome band 16p13.11. Our results support the hypothesis that regions flanked by duplicons are enriched for copy number variations.

Child↗
PubMed2026

Intramuscular patient-derived xenografts achieve high engraftment rates in gastric cancer: implications for pharmacodynamic testing and genomic biomarker discovery.

BACKGROUND: Gastric cancer (GC) exhibits marked inter-patient heterogeneity, limiting empirical chemotherapy efficacy. Patient-derived xenograft (PDX) models preserve the molecular features of parental tumors and can serve as pharmacodynamic surrogates, but conventional subcutaneous PDX suffers from low engraftment rates. This study evaluated an optimized intramuscular PDX platform for individualized drug testing in GC and applied whole exome sequencing (WES) for biomarker identification (Clinical trial registry: ChiCTR-OOC-17012731). MATERIALS AND METHODS: Ninety-eight treatment-naive GC patients were enrolled between April 2018 and December 2020. Fresh tumor tissues were engrafted into NCG mice by intramuscular transplantation. Drug efficacy was evaluated using tumor cell necrosis rate and Ki-67 expression. WES was performed on 32 engrafted tumorgrafts to characterize driver mutations in fast- and slow-growing subgroups. RESULTS: An engraftment rate of 71.7% (43/60) was achieved, substantially exceeding rates reported in prior studies. Clinical characteristics were independent of engraftment success and outgrowth time (all p > 0.05). Fast- and slow-growing tumorgrafts diverged in frequently altered genes: KMT2C, APOB, CDK12 and MSH2 predominated in fast-growing grafts, whereas TP53, CHD3 and TET2 were enriched in slow-growing grafts. Slow-growing tumorgrafts correlated with longer progression-free survival (p = 0.02). PDX-guided treatment was associated with improved prognosis. CONCLUSIONS: Intramuscular transplantation into NCG mice yields high engraftment rates for GC PDX. PDX-guided chemotherapy selection is associated with favorable outcomes. Driver mutation divergence between fast- and slow-growing tumorgrafts provides candidate prognostic biomarkers.

Animals↗
PubMed1994

Rapidly evolving repetitive DNAs in a conservative genome: a test of factors that affect chromosomal evolution.

The hypothesis that tandemly repeated DNA sequences may facilitate chromosomal rearrangements was tested by comparing a conservatively evolving karyotype of a bat species (Macrotus waterhousii) with data published for a rapidly evolving karyotype of an equid species (Equus zebra). Empirical data generated from the phylogenetic screening of rapidly evolving repetitive DNAs from approximately 0.1% of the M. waterhousii genome showed only one sequence that was repetitive in M. waterhousii but low in copy number or absent from the outgroup Artibeus jamaicensis. This compares to 34 such clones containing sequences which were repetitive in E. zebra but were low in copy number or absent from the outgroup Ceratotherium simum. The bat sequence represents a single family of repeated sequences, whereas six families of sequences were identified in E. zebra. Southern blot analysis suggested that the sequence from M. waterhousii is interspersed rather than tandemly repeated, as are the sequences in E. zebra. These data support the above hypothesis and suggest that species with conservatively evolving karyotypes have fewer numbers and families of rapidly evolving DNA sequences than do species such as the equids that possess a karyotype that is considered to have undergone rapid karyotypic evolution.

Animals↗
PubMed1997

[Anti-hepatitis C prevalence and incidence in 2.8 million blood donors in Lower Saxony--residual transfusion-associated HCV risk].

561 out of 2,777,021 blood donations from 582,655 donors tested confirmed positive for anti-HCV (RIBA II or Matrix Dot), 549 of them at their first donation, in their first HCV test ever, or in the first HCV test with a new, more sensitive test generation. Thus, our anti-HCV prevalence is 0.037% or 1 in 2,679 donations; among first-time donations it is five times higher than among repeat donations. Twelve repeat donors seroconverted, yielding an anti-HCV incidence of 0.0008% or 1 in 122,570 repeat donations and a seroconversion rate of 2.32 per 10(5) repeat donor person-years. The residual risk associated with transfusion of blood for repeat donors amounts to 5.2 per 10(6) repeat donations. We estimate a risk reduction from introduction of direct virus genome testing after PCR to be at 3.7 per 10(6) repeat donations. Look-backs among recipients of the last seronegative blood products from 12 donors with subsequent seroconversion revealed no recipient infection. Thus, today the residual risk for HCV transmission through transfusion of blood components obtained from Lower Saxony blood donors is quite low. The added safety from direct virus genome testing after PCR is considered extremely low, which casts doubt on the cost-effectiveness of such a measure.

Blood Donors↗
PubMed2005

Microarray based comparative genomic hybridization testing in deletion bearing patients with Angelman syndrome: genotype-phenotype correlations.

BACKGROUND: Angelman syndrome (AS) is a neurodevelopmental disorder characterised by severe mental retardation, dysmorphic features, ataxia, seizures, and typical behavioural characteristics, including a happy sociable disposition. AS is caused by maternal deficiency of UBE3A (E6 associated protein ubiquitin protein ligase 3A gene), located in an imprinted region on chromosome 15q11-q13. Although there are four different molecular types of AS, deletions of the 15q11-q13 region account for approximately 70% of the AS patients. These deletions are usually detected by fluorescence in situ hybridisation studies. The deletions can also be subclassified based on their size into class I and class II, with the former being larger and encompassing the latter. METHODS: We studied 22 patients with AS due to microdeletions using a microarray based comparative genomic hybridisation (array CGH) assay to define the deletions and analysed their phenotypic severity, especially expression of the autism phenotype, in order to establish clinical correlations. RESULTS: Overall, children with larger, class I deletions were significantly more likely to meet criteria for autism, had lower cognitive scores, and lower expressive language scores compared with children with smaller, class II deletions. Children with class I deletions also required more medications to control their seizures than did those in the class II group. CONCLUSIONS: There are four known genes (NIPA1, NIPA2, CYFIP1, & GCP5) that are affected by class I but not class II deletions, thus raising the possibility of a role for these genes in autism as well as the development of expressive language skills.

Angelman Syndrome↗
PubMed2004

The role of cost-effectiveness analysis in the era of pharmacogenomics.

The broad availability of genetic information and technologies heralds an era when practitioners will utilise genomic testing to individualise patients' care. Pharmacogenomics uses a spectrum of approaches to explore the association of genetic variation with drug efficacy or toxicity. Investigators have described a broad array of genetic polymorphisms that confer inter-individual differences in drug response. Pharmacogenomics offers the potential to improve drug effectiveness, reduce adverse drug reactions and provide cost-effective care. However, it has had little impact on current clinical practice and the economic implications of pharmacogenomics remain unclear. Assessing the incremental cost effectiveness of a pharmacogenomic strategy involves examination of factors associated with the genotype of interest, the genomic test, the disease state and the treatment. A pharmacogenomic strategy is likely to be cost effective when: (i) the polymorphism under consideration is prevalent in the population and has a high degree of penetrance; (ii) genetic testing is highly sensitive and specific, and less costly alternative tests that could be used to individualise therapy are not readily available; (iii) the disease state involves outcomes with significant morbidity or mortality if left untreated; and (iv) the treatment involves significant outcomes and/or costs that can be impacted by genotype-individualised therapy. We foresee pharmacogenomic applications being particularly relevant for drugs: with a narrow therapeutic index or a high degree of variability in inter-individual response; where there are limitations in current methods for monitoring their adverse effects and treatment responses; and where there are few alternative treatment options. Because of the characteristics of chemotherapeutic agents and the severity of clinical outcomes in cancer, oncology appears to be one of the most appropriate disease areas for the application of pharmacogenomics. We have developed a framework which can assist researchers, pharmacists, physicians, and policy makers in evaluating the implications of specific strategies, and identifying when formal cost-effectiveness analyses should be conducted to quantitatively evaluate the benefits of pharmacogenomics.

Cost-Benefit Analysis↗
PubMed2001

[A case of spinocerebellar ataxia type 6 with hypochondriasis and severe parkinsonism].

We report a case of 68-year-old woman who was diagnosed spinocerebellar ataxia type 6 (SCA 6) by genomic testing. She presented hypochondriasis, parkinsonism, and ataxia. Since the age of 60, she noted difficulty in walking due to dizziness, and MRI showed minimal cerebellar atrophy. She became unable to walk without assistance at the age 67. She was referred to us when she was 68 years old. She had no family history of cerebellar ataxia, and her general physical examination was normal. Her speech was fluent, with neither slurring nor scanning, and she complained of much anxiety regarding her physical condition and was diagnosed as having hypochondriasis. Neurological examination revealed parkinsonism consisting of small steppage gait, mask-like face, akinesia, rigidity of neck and limbs, and postural instability. She also showed cerebellar signs such as saccadic smooth pursuit, ataxia of upper and lower limbs, and increased tendon reflexes. Her parkinsonism had developed slowly and symmetrically yet she showed a lack of response to levodopa. Our results suggest that the genomic testing is useful for differential diagnosis for the diseases presenting ataxia and parkinsonism, even if the family history is negative.

Aged↗
PubMed2026

Real-world clinical utility of exome sequencing in pediatric drug-resistant epilepsy: Experience from a tertiary center in Thailand.

BACKGROUND: Genomic testing has increasingly contributed to the diagnosis and management of pediatric drug-resistant epilepsy (DRE), particularly in patients with suspected genetic etiologies. This study evaluated the diagnostic yield and real- world clinical utility of whole-exome sequencing (WES) in children with DRE. METHODS: Children with DRE and seizure onset before 15 years of age were enrolled between January 2020 and December 2023. Clinical data, including demographics, seizure characteristics, developmental history, electroencephalography (EEG), brain magnetic resonance imaging (MRI), and prior investigations, were reviewed. WES was performed in all probands and, when available, their parents. Variants were interpreted according to standard guidelines. Clinical utility and 1-year seizure and developmental outcomes were assessed from follow-up records. RESULTS: Fifty-six patients (23 males, 33 females) were included. The median age at seizure onset was 1 year (interquartile range [IQR] 0.3-4 years), and 96.4% had developmental comorbidities. Pathogenic or likely pathogenic variants were identified in 39% (22/56), with the highest diagnostic yield in children with seizure onset before 3 years of age. Channelopathies accounted for most genetically solved cases (68%), predominantly involving sodium channel genes. Genetic diagnoses provided clinical utility in 73% (16/22) of solved cases by guiding treatment and precision management. At 1-year follow-up, genetically solved patients showed more favorable seizure and developmental outcomes than those with genetically unsolved patients. CONCLUSION: WES achieved a 39% diagnostic yield and substantial clinical utility in pediatric DRE, particularly in early-onset and channelopathy-related disorders. These findings support early molecular diagnosis to facilitate genotype-informed management in appropriately selected children. However, the more favorable developmental and seizure outcomes observed in genetically solved patients should be interpreted with caution, as they may have been influenced by multiple factors beyond genetic diagnosis. In resource-limited settings, careful clinical phenotyping remains essential for treatment decisions and for prioritizing children for genomic testing.

Clinical utility↗
PubMed1990

Presence in invertebrate genomes of sequences characterized by the repetition of the triplet CCPurine.

In Drosophila melanogaster (Dm), polypeptidic domains have been found in different morphogenetic genes. Two types of them are characterized by the repetition of nucleotidic triplets: the M repeat (CAX) and the paired repeat (CAXCCX). In this paper we described a third type of repeat isolated from the genome of a Polychaete annelid: Owenia fusiformis. This repeat is characterized by the repetition of the triplet CCPurine. Phylogenetic studies showed the presence of this repeat in all the invertebrate genomes tested (eight copies in Dm genome) while we failed to detect it in vertebrate genomes.

Amino Acid Sequence↗
PubMed1999

Bunyavirus superinfection and segment reassortment in transovarially infected mosquitoes.

Rapid evolution of bunyaviruses may occur by RNA segment reassortment between closely related viruses. Reassortment between viruses occurs in dually infected mosquitoes when two different viruses are simultaneously ingested or when the second virus is ingested within 2 days of the first virus. By 3 days after oral infection, interference to superinfection occurs, thus limiting the potential for evolution. Aedes triseriatus mosquitoes can also be transovarially infected (TI+) with LaCrosse (LAC) virus. In these studies, the potential for oral superinfection of TI+ mosquitoes was assessed. Approximately 20% of mosquitoes TI+ with either a temperature-sensitive LAC virus or wild-type (wt) LAC virus became superinfected by ingesting blood meals containing wt LAC or snowshoe hare (SSH) viruses. LAC virus TI+ mosquitoes superinfected with SSH virus were detected by blot hybridization or RT-PCR. Viruses from these mosquitoes were plaque purified and genotyped using RT-PCR. Reassortant genomes were detected in 2.3% of the viruses genotyped, and 4.0% of the genomes tested were diploid for one genome segment.

Aedes↗
PubMed2026

Multigene testing to guide clinical adjuvant decisions in breast cancer: An overview focused on the assessment of the quality of evidence with the grading of recommendations assessment, development and evaluation (GRADE) approach.

Multigene tests have emerged as valuable tools in guiding adjuvant chemotherapy decisions for patients with ER-positive/HER2-negative early breast cancer. This study applied the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to assess the quality of evidence supporting the clinical utility of these tests. We focused on OncotypeDX® and MammaPrint®, the two tests evaluated in prospective randomized trials. The analysis was structured around the clinical question of whether these tests should be recommended for patients with ER-positive, HER2-negative, lymph node-negative or up to 3 lymph nodes-positive invasive breast cancer to guide adjuvant chemotherapy decisions. Our findings reveal that OncotypeDX® demonstrates high clinical utility in sparing chemotherapy for older/postmenopausal patients, with convincing quality of evidence for both node-negative and node-positive patients. The clinical utility of MammaPrint® appears more controversial, with conflicting results between node-negative and node-positive patients. A particularly critical aspect remains the clinical usefulness of these tests in younger/premenopausal women, where the benefit of adjuvant chemotherapy was shown but with potential biases in the study designs. Despite the established role of multigene tests and their availability in Italy since 2021, their uptake in clinical practice remains suboptimal. This formal appraisal of the clinical utility of genomic tests, particularly OncotypeDX®, aims to reinforce their fundamental role in personalizing adjuvant treatment decisions and optimizing resource allocation. The study underscores the importance of these tests in sparing unnecessary chemotherapy toxicities and costs, while emphasizing the need for further research to address remaining uncertainties, especially in younger patient populations.

Humans↗