Molecular Cytogenetics最新文献

{"title":"Whole genome uniparental isodisomy detected using single nucleotide polymorphism (SNP) microarray in molar pregnancy: a case report.","authors":"Onyinye O Okonkwo, Veronica Ortega, Sheila Kane, Galina Aldrete, Paulina Ramirez, Philip T Valente, Gopalrao V N Velagaleti","doi":"10.1186/s13039-025-00707-6","DOIUrl":"10.1186/s13039-025-00707-6","url":null,"abstract":"<p><strong>Background: </strong>Gestational trophoblastic neoplasms consist of complete and partial hydatidiform moles, both of which are considered aberrant conceptuses. Both conditions, complete hydatidiform mole (CHM) and partial hydatidiform mole (PHM), differ in histological characteristics, genetic origin and content and clinical features. CHM have a diploid karyotype, mostly 46,XX but lack maternal genetic contribution with all chromosomes of paternal origin. High-resolution SNP microarray testing is an efficient method used to determine the parental contribution of the genomic material in molar pregnancies and confirm the diagnosis.</p><p><strong>Case presentation: </strong>We present a case of CHM in a 43-year-old, G3P2Ab1 who presented to the emergency department with 2 episodes of heavy bleeding. Chromosome analysis showed a normal 46,XX karyotype but with a homozygous pericentric inversion on chromosome 9. High-resolution SNP microarray studies detected whole genome uniparental isodisomy.</p><p><strong>Conclusion: </strong>We present a case of CHM with homozygous pericentric inversion on chromosome 9 and whole genome uniparental isodisomy. This case illustrates the efficacy of high-resolution SNP microarray in confirming the diagnosis of CHM.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"4"},"PeriodicalIF":1.3,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11863443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143502866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence of CNVs on the X chromosome in patients with neurodevelopmental disorders.","authors":"Ekaterina N Tolmacheva, Anna A Kashevarova, Elizaveta A Fonova, Olga A Salyukova, Gulnara N Seitova, Lyudmila P Nazarenko, Anna A Agafonova, Larisa I Minaycheva, Ekaterina G Ravzhaeva, Valeria V Petrova, Maria E Lopatkina, Elena O Belyaeva, Svetlana L Vovk, Dmitry A Fedotov, Oksana Y Vasilyeva, Nikolay A Skryabin, Igor N Lebedev","doi":"10.1186/s13039-025-00703-w","DOIUrl":"10.1186/s13039-025-00703-w","url":null,"abstract":"<p><strong>Background: </strong>The X chromosome is enriched with genes related to brain development, and the hemizygous state of these genes in men causes some difficulties in the clinical interpretation of copy number variations (CNVs). In this study, we present data on the frequency and spectrum of CNVs on the X chromosome in a cohort of patients with neurodevelopmental disorders (NDDs).</p><p><strong>Methods: </strong>Chromosomal microarray analysis was performed for 1175 patients with NDDs. CNVs were confirmed by real-time quantitative PCR. X chromosome inactivation was analysed by methyl-sensitive PCR. To determine the pathogenic significance of the CNVs, several criteria, including the origin (inherited or de novo), variant type (microdeletion or microduplication), and X chromosome inactivation pattern in asymptomatic and symptomatic carriers, were considered. Additionally, the spectrum, size and molecular bases of copy number changes in genes or gene regions involved in the development of the pathological phenotype in each patient were considered.</p><p><strong>Results: </strong>CNVs on the X chromosome were identified in 33 patients (2.8%). Duplications and triplications (27 cases) were four times more common than deletions (6 cases). In 74% of patients, CNVs were of maternal origin; in 10% they were of paternal origin; and in 16% they arose de novo. The frequency of skewed X inactivation among family members who were healthy carriers of pathogenic and likely pathogenic CNVs and variants of uncertain significance (VUSs) on the X chromosome was 23%. For the first time, we reported several CNVs, including a pathogenic microdeletion at Xq26.1q26.2 involving the ARHGAP36 gene and a microduplication at Xp22.2 involving the OFD1 gene, CONCLUSIONS: This study expands on the frequency and spectrum of CNVs in patients with NDDs. Pathogenic variants on the X chromosome were present in 15% of cases, LP in 12%, VUS in 57%, and LB in 16% of cases. Previously unreported CNVs aid in the identification of new structural variants and genes associated with X-linked intellectual disability. We propose to consider the X-chromosome inactivation status when assessing the pathogenetic significance of CNVs using the ACMG algorithm (American College of Medical Genetics).</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"3"},"PeriodicalIF":1.3,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preparing high-quality chromosome spreads from Crocus species for karyotyping and FISH.","authors":"Abdullah El-Nagish, Susan Liedtke, Sarah Breitenbach, Tony Heitkam","doi":"10.1186/s13039-025-00706-7","DOIUrl":"10.1186/s13039-025-00706-7","url":null,"abstract":"<p><strong>Background: </strong>The saffron-producing Crocus sativus (L.) and its wild relative C. cartwrightianus (Herb.) are key species for understanding genetic evolution in this genus. Molecular-cytogenetic methods, especially fluorescent in situ hybridization (FISH), are essential for exploring the genetic relationships in this genus. Yet, preparing high-quality chromosomes for FISH analysis across Crocus species remains difficult. A standardized protocol for achieving clear and well-separated mitotic chromosomes is still lacking. This study aimed to assess the effectiveness of pretreatments with four chromosome synchronization methods for optimal chromosome spread preparation in Crocus. Root tips of different Crocus species were treated with four chromosome preparation methods namely hydroxyurea-colchicine (HC), nitrous oxide (NO), hydroxyquinoline (HQ), and ice water (IW) pretreatments to investigate their effectiveness in producing high-quality mitotic chromosome spreads. Metaphases obtained by the four methods were analyzed to assess their quality and metaphase index.</p><p><strong>Results: </strong>Evaluation of 22,507 cells allowed us to confidently recommend a protocol for Crocus chromosome preparation. Among the methods, ice water pretreatment yielded the highest metaphase index (2.05%), more than doubling the results of HC (1.08%), NO (1.15%), and HQ (1.16%). Ice water-treated chromosomes exhibited better chromosome morphology, with relatively proper size, and non-overlapping chromosomes that were optimal for FISH analysis. Ice water pretreatment was also applied to C. cartwrightianus, the diploid progenitor of C. sativus, where it demonstrated similar efficacy. DAPI staining of chromosomes in both species allowed for clear visualization of intercalary and terminal heterochromatin. FISH analysis using 18S-5.8S-25S and 5S rDNA probes confirmed the utility of IW-prepared chromosome spreads for cytogenetic studies.</p><p><strong>Conclusions: </strong>We strongly recommend ice water pretreatment as a suitable and effective method for obtaining many metaphase spreads of high-quality in C. sativus and related species, particularly for applications involving a detailed cytogenetic analysis.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"2"},"PeriodicalIF":1.3,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic and genotypic insights into concurrent tertiary trisomy for 9p and 18p.","authors":"Carter A Wright, Angela E Scheuerle, Kathleen Wilson, Rolando García, Prasad Koduru","doi":"10.1186/s13039-025-00704-9","DOIUrl":"10.1186/s13039-025-00704-9","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Carriers of balanced reciprocal translocation are usually phenotypically normal; however, they have an increased risk of producing gametes with chromosomal imbalance through different types of meiotic segregation of the translocation quadrivalent. The genetically imbalanced gametes when they survive can result in embryos with chromosomal abnormalities. Here we report a family with two siblings inheriting partial trisomy for 9p and 18p concurrently resulting from a 3:1 meiotic segregation of a maternal balanced translocation involving chromosome 9q and 18p, and the associated phenotype.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;The family - case presentation: &lt;/strong&gt;The family was ascertained because of severe congenital anomalies in a newborn male (sibling 1). The karyotype of this patient was 47,XY,+del(9)(q13q34). Cytogenetic analysis revealed that the phenotypically normal mother harbored a balanced translocation 46,XX,t(9;18)(q13;p11.21). Chromosomal microarray analysis (CMA) of the abnormal child detected segmental trisomy for 9p and 18p. In conjunction with conventional cytogenetic results of the mother and CMA results of the affected child, the final karyotype of sibling one was 47,XY,+der(9)t(9;18) (q13;p11.22)dmat. arr[GRCh36] 9p24.3q13(199254_70163189)× 3, 18p11.32p11.22(131491_9640590)× 3; this resulted in segmental duplication of 69.96 Mb on 9pter-&gt;q13 and 9.51 Mb on 18p. There was a subsequent birth of a female sibling (sibling two) with multiple anomalies, including dysmorphic facial features, kidney aberration, cardiac defects, and abnormal brain MRI. The G-banded karyotype of this sibling was 47,XX,+del(9)(q13q34). The final karyotype of this sibling after CMA results was 47,XX,+der(9)t(9;18)(q13;p11.22)dmat. arr[GRCh37] 9p24.3p13.1(209020_38763958)× 3; 18p11.32p11.22(146484_9640912)× 3. The apparent discrepancy between the array results of the two siblings is attributed to difference in the design of array chips and genome builds used for these patients (NimbleGen/Roche v2.0 3-plex and GRCh36 for sibling one, and GGXChip + SNP array and GRCh37 of Agilent Technologies for sibling two). There are 182 OMIM genes in the duplicated region of 9p and 33 OMIM genes in the duplicated region of 18p which may have contributed to the clinical features of the affected siblings.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;To our knowledge, we report the first two cases of concurrent partial trisomy 9p and 18p in the same family. This report adds more information about phenotypic effects of these chromosomal copy number gains and supports chromosomal microarray analysis as the standard for precise identification or demarking regions of duplications, particularly when the translocation involves at least one subterminal segment. In view of the recurring infants with congenital anomalies the couple may benefit from prenatal chromosome analysis of future pregnancies or opting to assisted reproductive methods and transferring normal embryos for implan","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"18 1","pages":"1"},"PeriodicalIF":1.3,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11808968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance of cell free DNA as a screening tool based on the results of first trimester screening.","authors":"Mahtab Motevasselian, Mohammad Amin Omrani, Soraya Saleh Gargari, Sarang Younesi, Mohammad Mahdi Taheri Amin, Pourandokht Saadati, Soudabeh Jamali, Mohammad-Hossein Modarresi, Shahram Savad, Majid Rahmani, Saloomeh Amidi, Saeed Delshad, Fariba Navidpour, Samira Chagheri, Yalda Mohammadi, Sheyda Khalilian, Solat Eslami, Soudeh Ghafouri-Fard","doi":"10.1186/s13039-024-00702-3","DOIUrl":"10.1186/s13039-024-00702-3","url":null,"abstract":"<p><p>The advent of non-invasive prenatal testing (NIPT) in the screening of fetal abnormalities has optimized prenatal care and decreased the rate of invasive diagnostic tests. In this retrospective descriptive study, we began with 1874 singleton pregnancies. After exclusion of some cases, the study cohort ended up with 1674 cases. We analyzed the performance of NIPT based on the results of first trimester screening (FTS) using serum screening combined with NT. The cases were also compared to diagnostic testing/pregnancy outcomes. Notably, in the subgroup with FTS risk < 1000, NIPT was reported to be normal in all cases with no false negative results. In the risk group of 1/300-1/1000, NIPT could detect all trisomy 21 cases with one false positive result. Moreover, in the risk group of 1/11 - 1/300, NIPT could detect all cases of trisomy 21, 13 and 18 with low false positive rate. However, the false positive rate for sex chromosomal abnormalities was high. Taken together, the current study confirms the applicability of NIPT as a tool for detection of fetal trisomies with high sensitivity and specificity. Yet, the high rate of false positive results for sex chromosome abnormalities should be considered in the interpretation of the results.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"33"},"PeriodicalIF":1.3,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662775/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of third-generation sequencing technology in the genetic testing of thalassemia.","authors":"Weihao Li, Yanchou Ye","doi":"10.1186/s13039-024-00701-4","DOIUrl":"10.1186/s13039-024-00701-4","url":null,"abstract":"<p><p>Thalassemia is an autosomal recessive genetic disorder and a common form of Hemoglobinopathy. It is classified into α-thalassemia and β-thalassemia. This disease is mainly prevalent in tropical and subtropical regions, including southern China. Severe α-thalassemia and intermediate α-thalassemia are among the most common birth defects in southern China. Intermediate α-thalassemia, also known as Hb H disease, is characterized by moderate anemia. Severe α-thalassemia, also known as Hb Bart's Hydrops fetalis syndrome, is a fatal condition. Infants with severe β-thalassemia do not show symptoms at birth but develop severe anemia later, requiring expensive treatment. Most untreated patients with severe β-thalassemia die in early childhood. Screening for thalassemia carriers and genetic diagnosis in high-prevalence areas significantly reduce the incidence of severe thalassemia. This review aims to summarize the genetic diagnostic approaches for thalassemia. Conventional genetic testing methods can identify 95-98% of thalassemia carriers but may miss rare thalassemia genotypes. Third-Generation Sequencing offers significant advantages in complementing other genetic diagnostic approaches, providing a basis for genetic counseling and prenatal diagnosis.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"32"},"PeriodicalIF":1.3,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical and genomic profiling of a patient with a de novo ring chromosome 18: a case report highlighting autoimmune and neurological implications.","authors":"Annalaura Montanari, Paola Caforio, Annalisa Paparella, Paola Casieri, Maria Cristina Nuzzi, Maria Fatima Antonucci, Claudia Rita Catacchio, Marilina Tampoia, Mattia Gentile, Roberta Bucci, Valerio Cecinati, Angelo Cellamare, Francesca Antonacci","doi":"10.1186/s13039-024-00700-5","DOIUrl":"10.1186/s13039-024-00700-5","url":null,"abstract":"<p><p>Ring chromosome 18 (r(18)) is a rare chromosomal abnormality characterized by the circular rearrangement of chromosome 18, which presents significant challenges in genotype-phenotype correlations due to variability in deletions across the 18p and 18q arms. We report the case of a pediatric patient with a de novo ring chromosome 18, diagnosed by karyotype analysis and confirmed by high-resolution SNP arrays. The patient exhibited pathogenic copy number variants (CNVs) in the 18p11.32p11.22 and 18q23 regions, involving 36 and 10 OMIM genes, respectively. Clinically, the patient presented with hypothyroidism secondary to autoimmune thyroiditis, autoimmune hepatitis type II, and genetic predisposition to celiac disease and insulin-dependent diabetes mellitus (IDDM) along with notable dysmorphic features. The 18q microdeletion encompasses the MBP gene, involved in the development and functionality of the nervous system, as supported by hypotonia and gliosis shown by the MRI. This case highlights the complex interplay between genetic imbalances on chromosome 18 and autoimmune phenotypes, emphasizing the need for ongoing research to elucidate underlying mechanisms and optimize clinical management for individuals with r(18).</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"31"},"PeriodicalIF":1.3,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11619688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142786229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interstitial 11q deletion in a patient with Sprengel's deformity: a case report and review of the literature.","authors":"Dhekra Ismail, Lilia Kraoua, Sylvie Jaillard, Hela Bellil, Mohamed Zairi, Faouzi Maazoul, Ridha Mrad, Mohamed Nabil Nessib, Mediha Trabelsi","doi":"10.1186/s13039-024-00695-z","DOIUrl":"10.1186/s13039-024-00695-z","url":null,"abstract":"<p><strong>Background: </strong>Interstitial chromosome 11 long arm deletions (11q13-q23) represent a rare cytogenetic abnormality characterized by non-specific clinical features including intellectual disability and several malformations without a clear genotype-phenotype correlation. We describe the first case of interstitial 11q deletion identified in a boy with Sprengel's deformity and provide a review of the literature.</p><p><strong>Case presentation: </strong>We report a 9-year-old boy with congenital scapular deformity, iris and chorioretinal coloboma, normal intelligence, and a history of mild motor development delay. The karyotype showed a de novo large 11q deletion. Fluorescence in situ hybridization (FISH) confirmed that the deletion is interstitial, and array comparative genomic hybridization (aCGH) revealed a loss of 25.8 Mb encompassing the 11q14.1-q22.3 region.</p><p><strong>Conclusions: </strong>The present case and the literature review of 61 previously published cases highlight the clinical heterogeneity and the lack of genotype-phenotype correlation in interstitial 11q deletions. Sprengel's deformity found in our patient might be a new finding in 11q deletions or, more probably, a fortuitous association.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"30"},"PeriodicalIF":1.3,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Insights into avian molecular cytogenetics-with reptilian comparisons.","authors":"Darren K Griffin, Rafael Kretschmer, Kornsorn Srikulnath, Worapong Singchat, Rebecca E O'Connor, Michael N Romanov","doi":"10.1186/s13039-024-00699-9","DOIUrl":"10.1186/s13039-024-00699-9","url":null,"abstract":"","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"29"},"PeriodicalIF":1.3,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11583397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Precision oncology platforms: practical strategies for genomic database utilization in cancer treatment.","authors":"Antonia A Gazola, William Lautert-Dutra, Leticia Frohlich Archangelo, Rodolfo B Dos Reis, Jeremy A Squire","doi":"10.1186/s13039-024-00698-w","DOIUrl":"10.1186/s13039-024-00698-w","url":null,"abstract":"<p><p>In recent years, the expansion of molecularly targeted cancer therapies has significantly advanced precision oncology. Parallel developments in next-generation sequencing (NGS) technologies have also improved precision oncology applications, making genomic analysis of tumors more affordable and accessible. Targeted NGS panels now enable the rapid identification of diverse actionable mutations, requiring clinicians to efficiently assess the predictive value of cancer biomarkers for specific treatments. The urgency for timely and accurate decision-making in oncology emphasizes the importance of reliable precision oncology software. Online clinical decision-making tools and associated cancer databases have been designed by consolidating genomic data into standardized, accessible formats. These new platforms are highly integrated and crucial for identifying actionable somatic genomic biomarkers essential for tumor survival, determining corresponding drug targets, and selecting appropriate treatments based on the mutational profile of each patient's tumor. To help oncologists and translational cancer researchers unfamiliar with these tools, we review the utility, accuracy, and comprehensiveness of several commonly used precision medicine software options currently available. Our analysis categorized selected genomic databases based on their primary content, utility, and how well they provide practical guidance for interpreting somatic biomarker data. We identified several comprehensive, mostly open-access platforms that are easy to use for genetic biomarker searches, each with unique features and limitations. Among the precision oncology tools we evaluated, we found MyCancerGenome and OncoKB to be the first choice, offering comprehensive, accurate up-to-date information on the clinical significance of somatic mutations. To illustrate the application of these precision oncology tools in clinical settings, we evaluated three case studies to see how use of the platforms could have influenced treatment planning. Most of the precision oncology software evaluated could be easily streamlined into clinical workflows to provide updated information on approved drugs and clinical trials related the actionable mutations detected. Some platforms were very intuitive and easy to use, while others, often developed in smaller academic settings, were more difficult to navigate and may not be updated consistently. Future enhancements, incorporating artificial intelligence algorithms, are likely to improve integration of the platforms with diverse big data sources, enabling more accurate predictions of potential therapeutic responses.</p>","PeriodicalId":19099,"journal":{"name":"Molecular Cytogenetics","volume":"17 1","pages":"28"},"PeriodicalIF":1.3,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11566986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}