Genomic Copy Number Variations Research Articles

Host Nuclear Genome Copy Number Variations Identify High-Risk Anal Precancers in People Living With HIV.

People living with HIV (PLWH) have substantially increased incidence of anal precancer and cancer. There are very little data regarding genomic disturbances in anal precancers among PLWH. In this study, specific chromosomal variants were identified in anal squamous intraepithelial lesions. Overall, 63 anal biopsy specimens (27 low-grade intraepithelial lesions [LSIL] and 36 high-grade intraepithelial lesions [HSIL]) were collected from PLWH obtained as part of anal cancer screening in our NYC-based health system. Data on patient demographics, anal cytological, and high-risk human papillomavirus (HR-HPV) diagnoses were collected. Specimens were tested for a panel of chromosomal alterations associated with HPV-induced oncogenesis using fluorescence in situ hybridization, and analyses compared the associations of these alterations with clinical characteristics. Gains of 3q26, 5p15, 20q13, and cen7 were detected in 42%, 31%, 31%, and 19% of HSIL compared with 7%, 0%, 4%, and 0% of LSIL, respectively. If at least 1 abnormality was observed, 89% had a 3q26 gain. In lesions with 5p15 gains, 20q13 gains co-occurred in 91% of cases, while cen7 gain only co-occurred with the other 3 alterations. The sensitivity and specificity of any alteration to predict HSIL were 47% (95% CI: 30%-65%) and 93% (95% CI: 76%-99%), respectively. Genomic alterations seen in HPV-associated cancers may help distinguish anal LSIL from HSIL. 3q26 amplification may be an early component of anal carcinogenesis, preceding 5p16, 20q13, and/or chr7. Insights into potential genomic biomarkers for discriminating high-risk anal precancers are shared.

Identification of necroptosis-related gene signatures for predicting the prognosis of ovarian cancer

Ovarian cancer (OC) is one of the most prevalent and fatal malignant tumors of the female reproductive system. Our research aimed to develop a prognostic model to assist inclinical treatment decision-making.Utilizing data from The Cancer Genome Atlas (TCGA) and copy number variation (CNV) data from the University of California Santa Cruz (UCSC) database, we conducted analyses of differentially expressed genes (DEGs), gene function, and tumor microenvironment (TME) scores in various clusters of OC samples.Next, we classified participants into low-risk and high-risk groups based on the median risk score, thereby dividing both the training group and the entire group accordingly. Overall survival (OS) was significantly reduced in the high-risk group, and two independent prognostic factors were identified: age and risk score. Additionally, three genes—C-X-C Motif Chemokine Ligand 10 (CXCL10), RELB, and Caspase-3 (CASP3)—emerged as potential candidates for an independent prognostic signature with acceptable prognostic value. In Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, pathways related to immune responses and inflammatory cell chemotaxis were identified. Cellular experiments further validated the reliability and precision of our findings. In conclusion, necroptosis-related genes play critical roles in tumor immunity, and our model introduces a novel strategy for predicting the prognosis of OC patients.

Clinical phenotype of a Kallmann syndrome patient with IL17RD and CPEB4 variants.

This study aimed to characterize the clinical phenotype and genetic variations in patients with Kallmann syndrome (KS). This study involved the collection and analysis of clinical data from an individual with sporadic KS. Following this, peripheral blood samples were obtained from the patient and his parents. Genomic deoxyribonucleic acid was extracted and subjected to whole-exome sequencing and genomic copy number variation (CNV) detection. Finally, Sanger sequencing was performed to validate the suspected pathogenic variants. Whole-exome sequencing confirmed that the child carried both the IL17RD variant (c.2101G>A, p.Gly701Ser) inherited from the mother and the new CPEB4 variant (c.1414C>T, p.Arg472*). No pathogenic CNVs were identified in CNV testing. Bioinformatics analysis shows that the IL17RD protein undergoing Gly701Ser mutation and is speculated to be phosphorylated and modified, thereby disrupting fibroblast growth factor signaling. This study also suggested that the CPEB4 might play a crucial role in the key signaling process affecting olfactory bulb morphogenesis. Overall, the findings of this study broaden the gene expression profile of KS-related pathogenic genes. This offers a new avenue for exploring the pathogenic mechanism of KS and provides valuable insights for precise clinical diagnosis and treatment strategies for this condition.

Novel copy number variations and phenotypes of infantile epileptic spasms syndrome.

We summarize the copy number variations (CNVs) and phenotype spectrum of infantile epileptic spasms syndrome (IESS) in a Chinese cohort. The CNVs were identified by genomic copy number variation sequencing. The CNVs and clinical data were analyzed. 74 IESS children with CNVs were enrolled. 35 kinds of CNVs were identified. There were 11 deletions and 5 duplications not reported previously in IESS, including 2 CNVs not reported in epilepsy. 87.8% were de novo, 9.5% were inherited from mother and 2.7% from father. Mosaicism occurred in one patient with Xq21.31q25 duplication. 16.2% (12/74) were 1p36 deletion, and 20.3% (15/74) were 15q11-q13 duplication. The age of seizure onset ranged from 17 days to 24 months. Seizure types included epileptic spasms, focal seizures, tonic seizures, and myoclonic seizures. All patients displayed developmental delay. Additional features included craniofacial anomaly, microcephaly, congenital heart defects, and hemangioma. 29.7% of patients were seizure-free for more than 12 months, and 70.3% still had seizures after trying 2 or more anti-seizure medications. In conclusion, CNVs is a prominent etiology of IESS. 1p36 deletion and 15q duplication occurred most frequently. CNV detection should be performed in patients with IESS of unknown causes, especially in children with craniofacial anomalies and microcephaly.

Abstract 2337: Accelerated optical genome mapping analysis with Stratys Compute and Guided Assembly

Abstract Background Optical genome maps (OGM) from Bionano enable the detection of genomic structural and copy number variants that cannot be detected by next-generation sequencing (NGS) technologies and are often missed by conventional cytogenetic techniques. Bionano has developed bioinformatics pipelines for calling structural and copy number variants including the Bionano Solve de novo assembly pipeline for constitutional analysis and the Rare Variant Analysis (RVA) pipeline for low-allele-fraction cancer applications. Both pipelines are computationally intensive and currently take 5-10 hours on the latest generation of the Bionano Saphyr® Compute which is deployed as a four-node compute cluster and requires significant IT resources. Methods To increase throughput and simplify the deployment of the compute resources needed to support the Stratys™ optical genome mapping instrument, Bionano has developed Stratys™ Compute. Stratys Compute improves both compute and analytical performance by adapting compute-intensive stages in the Solve pipeline to run on GPUs and by developing the Guided Assembly pipeline. Stratys Compute is powered by state-of-the-art NVIDIA RTX 6000 Ada generation cards and CUDA-optimized refinement, alignment, and structural variation detection kernels to accelerate OGM analysis. Stratys Compute is a standalone workstation placed adjacent to Stratys instrument. This will minimize the IT footprint and bypass the integration with the customer site’s data center. We have incorporated these optimizations into the new Guided Assembly pipeline, which aims to combine the low-allele fraction detection capability of the RVA pipeline with the whole genome coverage and ability to detect smaller structural variants enabled by the de novo assembly pipeline. The Guided Assembly pipeline uses the reference genome as an initial seed followed by extension, refinement, and structural variant calling. This new analysis method has been evaluated through comparison to previous results from both existing pipelines and standard benchmarking datasets used to estimate structural variant calling performance and is deployed on Stratys Compute for both constitutional and low allele-fraction applications. Results Guided Assembly has been adapted to run on GPU hardware in a simplified compute tower that can be deployed to a lab along with the Stratys instrument without the need for a dedicated server room. We found concordance between the guided assembly results and our previous de novo and RVA pipeline results. We also found increased sensitivity at low allele fractions for detecting insertion variants smaller than 5 kb and larger than 200 kb while finding equivalent performance for other variant types with the updated methods. The accelerated Guided Assembly for constitutional and low-allele-fraction applications will be available to early access customers in Q4 2023 with full commercial release in Q2 2024. Citation Format: Damla Senol Cali, Thomas Anantharaman, Martin Muggli, Samer Al-Saffar, Charles Schoonover, Neil Miller. Accelerated optical genome mapping analysis with Stratys Compute and Guided Assembly [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 2337.

Identification of a rare copy number polymorphic gain at 3q12.2 with candidate genes for familial endometriosis.

Endometriosis is a complex disease that affects 10-15% of women of reproductive age. Familial studies show that relatives of affected patients have a higher risk of developing the disease, implicating a genetic role for this disorder. Little is known about the impact of germline genomic copy number variant (CNV) polymorphisms on the heredity of the disease. In this study, we describe a rare CNV identified in two sisters with familial endometriosis, which contain genes that may increase the susceptibility and progression of this disease. We investigated the presence of CNVs from the endometrium and blood of the sisters with endometriosis and normal endometrium of five women as controls without the disease using array-CGH through the Agilent 2x400K platform. We excluded common CNVs that were present in the database of genomic variation. We identified, in both sisters, a rare CNV gain affecting 113kb at band 3q12.2 involving two candidate genes: ADGRG7 and TFG. The CNV gain was validated by qPCR. ADGRG7 is located at 3q12.2 and encodes a G protein-coupled receptor influencing the NF-kappaβ pathway. TFG participates in chromosomal translocations associated with hematologic tumor and soft tissue sarcomas, and is also involved in the NF-kappa B pathway. The CNV gain in this family provides a new candidate genetic marker for future familial endometriosis studies. Additional longitudinal studies of affected families must confirm any associations between this rare CNV gain and genes involved in the NF-kappaβ pathway in predisposition to endometriosis.

46, XX disorder of sexual development associated with mixed germ cell tumor of the prostate: a rare case report

BackgroundExtragonadal germ cell tumors originating from the prostate are exceptionally rare. To the best of our knowledge, there have been no reported cases of mixed germ cell tumors in individuals with 46 XX disorder of sex development. In this study, we conducted a comprehensive analysis using whole genome sequencing to investigate the clinicopathological and molecular genetic characteristics of a submitted case, with the objective of elucidating its underlying pathogenesis.Case presentationA 40-year-old male patient was diagnosed with a combination of 46, XX disorder of sex development and a primary prostate mixed germ cell tumor with yolk sac tumor and teratoma components. Whole-genome sequencing revealed that the tumor cells had a high somatic mutational load. Analysis of genomic structural variations and copy number variants confirmed the patient's karyotype as 46, XX (SRY +). Additionally, the patient exhibited short stature, small bilateral testes, slightly enlarged breasts, elevated serum alpha-fetoprotein concentrations, elevated follicle-stimulating hormone and luteinizing hormone levels, and low testosterone levels.DiscussionA case of 46, XX disorder of sex development, along with a primary prostatic mixed germ cell tumor, was diagnosed. This diagnosis has contributed to advancing our understanding of the genetic and phenotypic profile of the disease and may provide some insights for its treatment.

(245) Surveying the Genomic Landscape of Peyronie's Disease: A Study of 22 Cases

Abstract Introduction Since its description in 1743 by François de la Peyronie, penile fibromatosis continues to present an elusive pathogenesis. One of its distinguishing characteristics is the excessive proliferation of fibrogenic myofibroblasts, resulting in the formation of dense fibrous plaques that disrupt the normal cytoarchitecture of the tunica albuginea, giving rise to penile abnormalities. The possible clonal nature of the disease has been investigated by many studies and some have identified occasional karyotypic abnormalities, most commonly involving chromosomes 7, 8, 17, 18, X and Y (Mulhal JP et al 2004). Objective This study aimed to comprehensively analyze the genomic landscape of Peyronie's disease in a significant number of cases using a whole genome copy number variation assay (CNV). The objective was to identify any recurrent chromosomal gains or losses that could shed light on the pathogenesis of this disease, including the potential identification of an underlying clonal process. Methods Thirty-nine surgical specimens were retrospectively examined from men diagnosed with Peyronie's disease, collected between 1992 and 2022 (median age: 56 years, range: 17-73). The study was conducted under the approval of the Institutional Review Board (IRB # 22-006924). Tissue samples were fixed in 10% buffered formalin, embedded in paraffin, and subsequently subjected to histologic review and DNA analysis. DNA extraction followed standard protocols. Among the samples, 22 contained high-quality material suitable for CNV array analysis using the OncoScan SNV array, which encompassed approximately 900 genes/loci with a resolution of 50-125 kb. Additionally, the array included a somatic mutation panel targeting nine cancer-related genes. Results No significant loss or gain of chromosomal material was identified in the twenty-two cases analyzed. However, the somatic mutation panel revealed potential unconfirmed DNA mutations in NRAS, EGFR, and TP53. Ongoing studies are being conducted to confirm these mutations. Conclusions The etiology and pathogenesis of Peyronie's disease remain unresolved, presenting a challenging area of research. However, the findings of this study provide evidence that major recurrent losses or gains of chromosomal material are unlikely to play a significant role in the pathogenesis of this disease. While shedding light on this aspect, it is crucial to acknowledge that further research is necessary to confirm and expand upon these initial observations. Disclosure No.

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits.

Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.

Data-driven information extraction and enrichment of molecular profiling data for cancer cell lines.

With the proliferation of research means and computational methodologies, published biomedical literature is growing exponentially in numbers and volume. Cancer cell lines are frequently used models in biological and medical research that are currently applied for a wide range of purposes, from studies of cellular mechanisms to drug development, which has led to a wealth of related data and publications. Sifting through large quantities of text to gather relevant information on cell lines of interest is tedious and extremely slow when performed by humans. Hence, novel computational information extraction and correlation mechanisms are required to boost meaningful knowledge extraction. In this work, we present the design, implementation, and application of a novel data extraction and exploration system. This system extracts deep semantic relations between textual entities from scientific literature to enrich existing structured clinical data concerning cancer cell lines. We introduce a new public data exploration portal, which enables automatic linking of genomic copy number variants plots with ranked, related entities such as affected genes. Each relation is accompanied by literature-derived evidences, allowing for deep, yet rapid, literature search, using existing structured data as a springboard. Our system is publicly available on the web at https://cancercelllines.org.

11q Gain with t(11;14) or Alone Were Associated with Poor Prognosis in Newly-Diagnosed Multiple Myeloma Patients By SNP-Array Analysis and FISH

t(11;14) is currently classified as a standard-risk genetic marker for newly diagnosed multiple myeloma (NDMM) patients. But some recent studies have suggested that t(11;14) may be an intermediate-risk marker in multiple myleoma (MM). The clinical significance of t(11;14) in MM is still controversial. Here, using high-resolution single nucleotide polymorphism-based mapping array (SNP-array) analysis and fluorescence in situ hybridization (FISH), the most common gained region of chromosome 11 was identified in 96/611 (15.7%) NDMM patients which located at 11q13.3-q25 (65.7Mb in size and contains 622 genes including CCND1). It demonstrated a statistically significant coexisting with t (11;14) (p<0.001), complex karyotypes (involves at least 6 chromosomes) (p<0.001), high plasma cell ratio in bone marrow (p=0.001) and poor response to VRD (bortezomib, lenalidomide, dexamethasone) treatment (p<0.001), but mutually exclusive with monosome 13, del(13q14), dup1q21 and t (4;14). When exploring the correlation of t(11;14) with genomic copy number variations (CNAs), it was also indicated that t(11;14) was most closely related to 11q gain (39%), while negatively correlated with others including gain of 1q and chromosome 3, 5, 6, 7, 9, 11, 15, 19, loss of 1p, 12p, 14q and chromosome 13 and 22. With a median follow up time of 22 months, survival analysis of 40 t(11;14) patients, 123 hyperdiploid (HRD) patients showed that 11q gain could have an adverse impact on the progression-free survival (PFS) in both groups. In t(11;14) subgroup, the median PFS (mPFS) were not reached, but PFS at 40 months were 60.9% vs 81.7% with 11q gain vs non-11q gain patients. In HRD subgroup, the mPFS were 23 months vs 49 months with 11q gain vs non-11q gain groups. Autologous hematopoietic stem cell transplantation (ASCT) can significantly improve the PFS of patients with t(11;14) and 11q gain (mPFS for transplant-eligible (TE) vs transplant-ineligible (TIE) patients were not reached vs 9 months, P=0.0067), but not helpful to 11q gain patients without t(11;14) (mPFS for TE vs TIE: 23 months vs 22 months, p=0.2137). Multivariate analysis confirmed that 11q gain was an independent adverse factor to PFS of MM with t(11;14) (Hazard ratio: 11.621, 95% CI: 1.027-131.507; p=0.048; n=37). Conclusions: Gain of 11q13.3-q25 is a reproducible chromosomal copy number abnormality in NDMM characterized by coexisting with t (11;14), complex karyotypes, higher plasma cell ratio in bone marrow and poor treatment response to VRD. t(11;14) patients with 11q gain had a poorer PFS compared to patients with t(11;14) only, mPFS was only 9 months for TIE patients. t(11;14) with 11q gain NDMM patients needs to be considered as high risk and ASCT could improve patients' survival.

CNVs Numbers Scoring System Was a Good Prognostic Risk Stratification for NDMM with Whole Genomic Mapping Array

Multiple myeloma (MM) is a genetically heterogeneous disease characterized by plasma cell clonal proliferation. Due to the potential complex cytogenetic abnormalities, the clinical progresses are heterogeneous. Thus, genome-wide identification of cytogenetic abnormalities is necessary given the limitations of traditional cytogenetic detecting methods. In this study, we utilized whole genomic mapping methods Cytoscan 750K array to analyze the genomic copy number variations (CNVs) of 611 Newly Diagnosed MM (NDMM) from The First Affiliated Hospital of Soochow University. The results showed that 95.3% of NDMM patients harbored the chromosome alterations including structural or numerical abnormalities, and most of them (67.3%) were accompanied both, including 23.7% with only structural abnormalities and 4.3% with only numerical abnormalities. The average number of CNV per patient was 9. In addition, we have identified 34 common CNV events with a frequency of ≥5%, 5 of which were high frequency (≥20%), including dup(1)(q21q44) (50.2%), del(14)(q22q32) (24.9%), del(1)(p31p12) (21.9%), del(13)(q12q22) (21.9%) and dup(19)(p13p12) (20.6%). Additionally, 6 CNVs with median frequency (≥15% and <20%) included dup(6)(p25p12) (16.9%), dup(9)(q21q34) (18.2%), del(16)(q12q24) (18.7%), del(8)(p23p12) (17.5%), dup(11)(q13q25) (15.7%) and del(22)(q11q12) (15.4%). And the other 23 CNVs were low frequency (<15%), including del(6)(q24q27) (14.6%), del(X)(p22q25) (14.1%), dup(X)(q28) (13.7%), dup(8) (q11q24) (12.6%), del(17)(p13p12) (11%) and so on. Most CNVs were closely related with clinical risk factors of MM such as LDH. Prognostic analysis based on the VRD treatment (n=353, the median follow-up was 22 months) showed that patients with only numerical abnormalities had a better progress free survival (PFS) outcome than that with structural abnormalities only or with both, although they seemed to have the similar overall survival (OS) rate. Furthermore, univariate analysis showed that 6 CNVs were correlated with poor PFS including 1q+, 4q-, 6q-, 12p-, 16q-, 17p-, and 5 CNVs were correlated with poor OS including 1p-, 4q-, 7p-, 12p-, 17p-. For the effect of counts of CNV events on MM prognosis, the receiver operating characteristic (ROC) curve analysis was performed to calculate the best cutoff, with a result of 23 CNV events. Therefore, MM patients were divided into 4 subgroups according to the counts of CNV they harbored, including high complexity group (CNVs≥23, n=32) which excluded patients with chromothripsis (more than 10 CNVs on the same chromosome) , median complexity group (10≤CNVs<23, n=168), low complexity group (1≤CNVs<10, n=324), and no CNVs group (n=73). The patients in high complexity group had the worst prognosis of PFS and OS (media PFS 18 months, media OS 29 months, P<0.001). As expected, some common high risk clinical factors such as 1q+, 17p-, DS III, ISS III, serum Ca++,β2-MG and plasma cells in BM were gradually increased among the group from low to high complexity, but decreased in the rate of complete remission (CR), which suggested that the risk classification system was reliable. Importantly, univariate and multivariate COX regression analysis showed that CNV≥23 was an independent prognostic risk factor affecting both PFS and OS in NDMM patients. Over all, we utilized a large MM cohort to identify recurrent and potential driver CNV events, and their correlation with prognosis. In addition, the count of CNVs in NDMM patient was creatively considered to be the basis for prognostic risk stratification.

Application of array comparative genomic hybridization in clinical diagnostics of intellectual disability/developmental delay in children

Background: This study was designed to analyze and evaluate the potential pathogenic genomic imbalance in children with unexplained intellectual disability (ID) and/or developmental delay (DD) and its association with phenotypes, and to investigate the value of array-based comparative genomic hybridization (array-CGH). Methods: A total of 72 Children with ID/DD were evaluated by array-CGH for detection of genomic copy number variations (CNVs). Results: The results of the array-CGH revealed that 10(14%) of the 72 patients had pathogenic CNVs, in that six cases had pathogenic CNV in a single chromosome, 2 cases had multiple microdeletions and 2 cases had combined microdeletion and microduplication, 2 cases had pathogenic CNVs in chromosome 1p36 and Xq28 region. One case had variation of unknown significance in chromosome region 15q11.2. Large bands of copy neutral loss of heterozygosity were detected in 2 cases comprising more than 10% of genome. Conclusions: Array-CGH being a high-throughput and rapid tool, allows for the etiological diagnosis in some of the children with unexplained ID/DD.

Mesonephric-like adenocarcinoma harbours characteristic copy number variations and a distinct DNA methylation signature closely related to mesonephric adenocarcinoma of the cervix.

Mesonephric-like adenocarcinoma (MLA) of the female genital tract is an uncommon histotype that can arise in both the endometrium and the ovary. The exact cell of origin and histogenesis currently remain unknown. Here, we investigated whole genome DNA methylation patterns and copy number variations (CNVs) in a series of MLAs in the context of a large cohort of various gynaecological carcinoma types. CNV analysis of 19 MLAs uncovered gains of chromosomes 1q (18/19, 95%), 10 (15/19, 79%), 12 (14/19, 74%), and 2 (10/19, 53%), as well as loss of chromosome 1p (7/19, 37%). Gains of chromosomes 1q, 10, and 12 were also identified in the majority of mesonephric adenocarcinomas of the uterine cervix (MAs) as well as subsets of endometrioid carcinomas (ECs) and low-grade serous carcinomas of the ovary (LGSCs) but only in a minority of serous carcinomas of the uterine corpus (USCs), clear cell carcinomas (CCCs), and tubo-ovarian high-grade serous carcinomas (HGSCs). While losses of chromosome 1p together with gains of chromosome 1q were also identified in both MA and LGSC, gains of chromosome 2 were almost exclusively identified in MLA and MA. Unsupervised hierarchical clustering and t-SNE analysis of DNA methylation data (Illumina EPIC array) identified a co-clustering for MLAs and MAs, which was distinct from clusters of ECs, USCs, CCCs, LGSCs, and HGSCs. Group-wise comparisons confirmed a close epigenetic relationship between MLA and MA. These findings, in conjunction with the established histological and immunophenotypical overlap, suggest bona fide mesonephric differentiation, and support a more precise terminology of mesonephric-type adenocarcinoma instead of MLA in these tumours. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Ribosomal, Telomere, and Mitochondrial Repeat Copy Number Variations in Female Genomes during Ovarian Stimulation and the Prediction of In Vitro Fertilization Outcome: A Pilot Study.

Individual risk assessment of assisted reproductive technologies is essential for personalized treatment strategies. Genetic and genomic indicators of the response to stress by cells could provide individual prognostic indicators for in vitro fertilization (IVF) success. Such indicators include the copy number of ribosomal genes (rDNA), which modulates the level of protein synthesis, and the abundance of mitochondrial DNA (mtDNA), which provides the cell with energy, while the content of telomere repeats (TRs) indicate the biological age. The contents of the three repeats in DNA isolated from blood leukocytes of 40 women before and after ovarian stimulation were assayed prior to IVF. Then, we divided the women into a successful IVF group, IVF+ (N = 17, 7 cases of twins), and a group of failed cases, IVF- (N = 23). The control group included 17 non-pregnant women with natural childbirth in the past. The nonradioactive quantitative hybridization (NQH) method was applied to assay the genome repeat contents. The number of rDNA copies in the IVF+ group was significantly higher than in the IVF- group (p < 10-8). The number of mtDNA copies in the IVF+ group also exceeded those in the IVF- group (p < 0.001), whereas the TR content in the two groups differed, albeit, non-significantly (p < 0.03). Following the ovarian stimulation, the rDNA copy numbers did not change, while the contents of the mtDNA and TR varied significantly. This pilot study has shown that rDNA abundance in blood leukocytes can be considered a stable and effective predictor. Very low numbers of ribosomal repeat copies (<330) entail a high risk of IVF failure. However, a combination of numerous mtDNA and TRs, provided that rDNA content is not very low, increases the probability of multiple pregnancies.

Co-Occurrence of Germline Genomic Variants and Copy Number Variations in Hereditary Breast and Colorectal Cancer Patients.

Hereditary Breast and Ovarian Cancer (HBOC) syndrome is an autosomal dominant disease associated with a high risk of developing breast, ovarian, and other malignancies. Lynch syndrome is caused by mutations in mismatch repair genes predisposing to colorectal and endometrial cancers, among others. A rare phenotype overlapping hereditary colorectal and breast cancer syndromes is poorly characterized. Three breast and colorectal cancer unrelated patients fulfilling clinical criteria for HBOC were tested by whole exome sequencing. A family history of colorectal cancer was reported in two patients (cases 2 and 3). Several variants and copy number variations were identified, which potentially contribute to the cancer risk or prognosis. All patients presented copy number imbalances encompassing PMS2 (two deletions and one duplication), a known gene involved in the DNA mismatch repair pathway. Two patients showed gains covering the POLE2 (cases 1 and 3), which is associated with DNA replication. Germline potentially damaging variants were found in PTCH1 (patient 3), MAT1A, and WRN (patient 2). Overall, concurrent genomic alterations were described that may increase the risk of cancer appearance in HBOC patients with breast and colorectal cancers.

Subcortical Brain Alterations in Carriers of Genomic Copy Number Variants.

Copy number variants (CNVs) are well-known genetic pleiotropic risk factors for multiple neurodevelopmental and psychiatric disorders (NPDs), including autism (ASD) and schizophrenia. Little is known about how different CNVs conferring risk for the same condition may affect subcortical brain structures and how these alterations relate to the level of disease risk conferred by CNVs. To fill this gap, the authors investigated gross volume, vertex-level thickness, and surface maps of subcortical structures in 11 CNVs and six NPDs. Subcortical structures were characterized using harmonized ENIGMA protocols in 675 CNV carriers (CNVs at 1q21.1, TAR, 13q12.12, 15q11.2, 16p11.2, 16p13.11, and 22q11.2; age range, 6-80 years; 340 males) and 782 control subjects (age range, 6-80 years; 387 males) as well as ENIGMA summary statistics for ASD, schizophrenia, attention deficit hyperactivity disorder, obsessive-compulsive disorder, bipolar disorder, and major depression. All CNVs showed alterations in at least one subcortical measure. Each structure was affected by at least two CNVs, and the hippocampus and amygdala were affected by five. Shape analyses detected subregional alterations that were averaged out in volume analyses. A common latent dimension was identified, characterized by opposing effects on the hippocampus/amygdala and putamen/pallidum, across CNVs and across NPDs. Effect sizes of CNVs on subcortical volume, thickness, and local surface area were correlated with their previously reported effect sizes on cognition and risk for ASD and schizophrenia. The findings demonstrate that subcortical alterations associated with CNVs show varying levels of similarities with those associated with neuropsychiatric conditions, as well distinct effects, with some CNVs clustering with adult-onset conditions and others with ASD. These findings provide insight into the long-standing questions of why CNVs at different genomic loci increase the risk for the same NPD and why a single CNV increases the risk for a diverse set of NPDs.

Clinicopathological significance of unraveling mitochondrial pathway alterations in non-small-cell lung cancer.

Early detection, accurate monitoring, and therapeutics are major problems in non-small-cell lung cancer (NSCLC) patients. We identified genomic copy number variation of a unique panel of 40 mitochondria-targeted genes in NSCLCs (GEOGSE #29365). Validation of mRNA expression of these molecules revealed an altered panel of 34 genes in lung adenocarcinomas (LUAD) and 36 genes in lung squamous cell carcinomas (LUSC). In the LUAD subtype (n = 533), we identified 29 upregulated and 5 downregulated genes, while in the LUSC subtype (n = 502), a panel of 30 upregulated and 6 downregulated genes were discovered. The majority of these genes are associated with mitochondrial protein transport, ferroptosis, calcium signaling, metabolism, OXPHOS function, TCA cycle, apoptosis, and MARylation. Altered mRNA expression of SLC25A4, ACSF2, MACROD1, and GCAT was associated with poor survival of the NSCLC patients. Progressive loss of SLC25A4 protein expression was confirmed in NSCLC tissues (n = 59), predicting poor survival of the patients. Forced overexpression of SLC25A4 in two LUAD cell lines inhibited their growth, viability, and migration. A significant association of the altered mitochondrial pathway genes with LC subtype-specific classical molecular signatures was observed, implicating the existence of nuclear-mitochondrial cross-talks. Key alteration signatures shared between LUAD and LUSC subtypes including SLC25A4, ACSF2, MACROD1, MDH2, LONP1, MTHFD2, and CA5A could be helpful in developing new biomarkers and therapeutics.

Diagnostic value of whole exome sequencing for patients with intellectual disability or global developmental delay

To assess the diagnostic value of whole exome sequencing (WES) for patients with intellectual disability (ID) or global developmental delay (GDD). 134 individuals with ID or GDD who presented at Chenzhou First People's Hospital between May 2018 and December 2021 were selected as the study subjects. WES was carried out on peripheral blood samples of the patients and their parents, and candidate variants were verified by Sanger sequencing, copy number variation sequencing (CNV-seq) and co-segregation analysis. The pathogenicity of the variants was predicted based on the guidelines from the American College of Medical Genetics and Genomics (ACMG). A total of 46 pathogenic single nucleotide variants (SNVs) and small insertion/deletion (InDel) variants, 11 pathogenic genomic copy number variants (CNVs), and 1 uniparental diploidy (UPD) were detected, which yielded an overall detection rate of 43.28% (58/134). The 46 pathogenic SNV/InDel have involved 62 mutation sites in 40 genes, among which MECP2 was the most frequent (n = 4). The 11 pathogenic CNVs have included 10 deletions and 1 duplication, which have ranged from 0.76 to 15.02 Mb. A loss of heterozygosity (LOH) region of approximately 15.62 Mb was detected in 15q11.2q12 region in a patient, which was validated as paternal UPD based on the result of trio-WES. The patient was ultimately diagnosed as Angelman syndrome. WES can detect not only SNV/InDel, but also CNV and LOH. By integrating family data, WES can accurately determine the origin of the variants and provide a useful tool for uncovering the genetic etiology of patients with ID or GDD.

Feasibility of Optical Genome Mapping in Cytogenetic Diagnostics of Hematological Neoplasms: A New Way to Look at DNA.

Optical genome mapping (OGM) is a new genome-wide technology that can reveal both structural genomic variations (SVs) and copy number variations (CNVs) in a single assay. OGM was initially employed to perform genome assembly and genome research, but it is now more widely used to study chromosome aberrations in genetic disorders and in human cancer. One of the most useful OGM applications is in hematological malignancies, where chromosomal rearrangements are frequent and conventional cytogenetic analysis alone is insufficient, necessitating further confirmation using ancillary techniques such as fluorescence in situ hybridization, chromosomal microarrays, or multiple ligation-dependent probe amplification. The first studies tested OGM efficiency and sensitivity for SV and CNV detection, comparing heterogeneous groups of lymphoid and myeloid hematological sample data with those obtained using standard cytogenetic diagnostic tests. Most of the work based on this innovative technology was focused on myelodysplastic syndromes (MDSs), acute myeloid leukemia (AML), and acute lymphoblastic leukemia (ALL), whereas little attention was paid to chronic lymphocytic leukemia (CLL) or multiple myeloma (MM), and none was paid to lymphomas. The studies showed that OGM can now be considered as a highly reliable method, concordant with standard cytogenetic techniques but able to detect novel clinically significant SVs, thus allowing better patient classification, prognostic stratification, and therapeutic choices in hematological malignancies.