Conventional Cytogenetic Techniques Research Articles

Determination of aneuploidy/polyploidy in Holstein cows with a history of abortion

Determination of aneuploidy/polyploidy in Holstein cows with a history of abortion

Optical Genome Mapping as a New Tool to Overcome Conventional Cytogenetics Limitations in Patients with Bone Marrow Failure.

Cytogenetic studies are essential in the diagnosis and follow up of patients with bone marrow failure syndromes (BMFSs), but obtaining good quality results is often challenging due to hypocellularity. Optical Genome Mapping (OGM), a novel technology capable of detecting most types chromosomal structural variants (SVs) at high resolution, is being increasingly used in many settings, including hematologic malignancies. Herein, we compared conventional cytogenetic techniques to OGM in 20 patients with diverse BMFSs. Twenty metaphases for the karyotype were only obtained in three subjects (15%), and no SVs were found in any of the samples. One patient with culture failure showed a gain in chromosome 1q by fluorescence in situ hybridization, which was confirmed by OGM. In contrast, OGM provided good quality results in all subjects, and SVs were detected in 14 of them (70%), mostly corresponding to cryptic submicroscopic alterations not observed by standard techniques. Therefore, OGM emerges as a powerful tool that provides complete and evaluable results in hypocellular BMFSs, reducing multiple tests into a single assay and overcoming some of the main limitations of conventional techniques. Furthermore, in addition to confirming the abnormalities detected by conventional techniques, OGM found new alterations beyond their detection limits.

Chromosomal organization of different repetitive sequences in four wasp species of the genus Trypoxylon Latreille (Hymenoptera: Crabronidae) and insights into the composition of wasp telomeres.

This study characterizes the chromosomal organization of DNA repetitive sequences and the karyotypic evolution in four representatives of the solitary wasp genus Trypoxylon using conventional and molecular cytogenetic techniques. Our findings present the first cytogenetic data for Trypoxylon rogenhoferi (2n = 30) and Trypoxylon albonigrum (2n = 32), while the karyotypes of Trypoxylon nitidum (2n = 30) and Trypoxylon lactitarse (2n = 30) were similar to those previously described. Fluorochrome staining and microsatellite distribution data revealed differences in the constitutive heterochromatin composition among species. Trypoxylon nitidum and T. albonigrum exhibited one major rDNA cluster, potentially representing an ancestral pattern for aculeate Hymenoptera, while T. rogenhoferi and T. lactitarse showed two pericentromeric rRNA gene sites, suggesting amplification events in their ancestral clade. The (TCAGG)n motif hybridized in the terminal regions of the chromosomes in all four Trypoxylon species, which may suggest that this sequence represents DNA telomeric repeat. Notably, the presence of this repetitive sequence in the centromeric regions of certain chromosome pairs in two species supports the hypothesis of chromosomal fusions or inversions in the ancestral karyotype of Trypoxylon. The study expands the chromosomal mapping data of repetitive sequences in wasps and offers insights into the dynamic evolutionary landscape of karyotypes in these insects.

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.

Optical Genome Mapping Reveals Novel Structural Variants in Lymphoblastic Lymphoma.

Accurate histologic and molecular genetic diagnosis is critical for the pathogenesis study of pediatric patients with lymphoblastic lymphoma (LBL). Optical genome mapping (OGM) as all-in-one process allows the detection of most major genomic risk markers, which addresses some of the limitations associated with conventional cytogenomic testing, such as low resolution and throughput, difficulty in ascertaining genomic localization, and orientation of segments in duplication, inversions, and insertions. Here, for the first time, we examined the cytogenetics of 5 children with LBL using OGM. OGM was used to analyze 5 samples of pediatric LBL patients treated according to the modified NHL-BFM95 backbone regimen. Whole-exon Sequencing (WES) was used to confirm the existence of structural variants (SVs) identified by OGM with potentially clinical significance on MGI Tech (DNBSEQ-T7) platform. According to the fusion exon sequences revealed by WES, the HBS1L :: AHI1 fusion mRNA in case 4 was amplified by cDNA-based PCR. In total, OGM identified 251 rare variants (67 insertions, 129 deletions, 3 inversion, 25 duplications, 15 intrachromosomal translocations, and 12 interchromosomal translocations) and 229 copy number variants calls (203 gains and 26 losses). Besides all of the reproducible and pathologically significant genomic SVs detected by conventional cytogenetic techniques, OGM identified more SVs with definite or potential pathologic significance that were not detected by traditional methods, including 2 new fusion genes, HBS1L :: AHI1 and GRIK1::NSDHL , which were confirmed by WES and/or Reverse Transcription-Polymerase Chain Reaction. Our results demonstrate the feasibility of OGM to detect genomic aberrations, which may play an important role in the occurrence and development of lymphomagenesis as an important driving factor.

Chromosome Banding Properties of Neogobius fluviatilis (Pallas, 1814) (Perciformes, Gobiidae)

The monkey goby, Neogobius fluviatilis (Pallas, 1814) that distributed in Türkiye was studied cytogenetically for the first time. In this context, diploid chromosome number, chromosome morphology and also chromosomal banding properties (C-banding and Ag-NOR staining) of N. fluviatilis were revealed out. Chromosome slides were prepared from head kidney cells according to the air-drying technique. Chromosome slides were observed under the microscope and metaphases were photographed. The chromosomes were measured by digital caliper and karyotype was arranged manually. The diploid chromosome number was found as 46. Karyotype was composed with all uniarmed chromosomes. Fundamental arm number was calculated as 46 too. No heteromorphic sex chromosomes were determined in the karyotype. C-bands were detected on the pericentromeres of almost all chromosomes. Otherwise, two Ag-NORs were found in the silver-stained metaphases. This study revealed out chromosomal properties of N. fluviatilis from Türkiye with conventional cytogenetic techniques. This report may improve the cytogenetic data of the genus Neogobius.

The Types and Frequencies of X Chromosome Abnormalities in Women with Reproductive Problems

Introduction: X chromosome architecture and integrity are essential for normal ovarian function. Both numerical and structural X chromosome abnormalities play an important role in female infertility. This study aimed to determine the types and frequency of X chromosome aberrations detected in women referred for cytogenetic investigation due to reproductive problems. Methods: 2,936 women (average age: 37.5 years) were enrolled in the present study. Peripheral blood karyotyping was performed by conventional cytogenetic techniques. For each woman, 20 G-banded metaphases were studied and in case of suspected mosaicism, analysis was extended to 100 metaphases. Results: 2,588/2,936 (88.15%) of women had a normal karyotype (46,XX), while 348/2,936 (11.85%) had an abnormal one. Thirty-two women (1.09%) carried autosomal chromosome abnormalities and 316 (10.76%) had X chromosome rearrangements. In 311/2,936 women (10.59%), X chromosome numerical aberrations were detected (low-level mosaicism), and in 5/2,936 cases (0.17%), X structural abnormalities (two with pericentric inversion, one with Xq deletion and two 45,X mosaics, one with an Xp deletion cell line and the other with isochromosome Xq cell line). Low-level X mosaicism was a common finding in women >35 years as compared to younger ones (92.93% vs. 7.07%), a finding consistent with loss of chromosome X with aging. Other X chromosome abnormalities were detected in younger women (32.3 ± 4.13 vs. 41.04 ± 4.5 years). The mean age of women with Turner-like phenotype was 28.75 ± 6.6 years. Conclusion: The study confirms that the incidence of X chromosome abnormalities is increased in women with fertility problems and that karyotype is the gold standard for their identification. Genetic counseling is recommended in these cases to provide information concerning available treatment and fertility options.

Optical Genome Mapping for Comprehensive Assessment of Chromosomal Aberrations and Discovery of New Fusion Genes in Pediatric B-Acute Lymphoblastic Leukemia

To assess the potential added value of Optical Genomic Mapping (OGM) for identifying chromosomal aberrations. We utilized Optical Genomic Mapping (OGM) to determine chromosomal aberrations in 46 children with B-cell Acute lymphoblastic leukemia ALL (B-ALL) and compared the results of OGM with conventional technologies. Partial detection results were verified by WGS and PCR. OGM showed a good concordance with conventional cytogenetic techniques in identifying the reproducible and pathologically significant genomic SVs. Two new fusion genes (LMNB1::PPP2R2B and TMEM272::KDM4B) were identified by OGM and verified by WGS and RT-PCR for the first time. OGM has a greater ability to detect complex chromosomal aberrations, refine complicated karyotypes, and identify more SVs. Several novel fusion genes and single-gene alterations, associated with definite or potential pathologic significance that had not been detected by traditional methods, were also identified. OGM addresses some of the limitations associated with conventional cytogenomic testing. This all-in-one process allows the detection of most major genomic risk markers in one test, which may have important meanings for the development of leukemia pathogenesis and targeted drugs.

Incidental Detection of a Chromosomal Aberration by Array-CGH in an Early Prenatal Diagnosis for Monogenic Disease on Coelomic Fluid.

Turner syndrome is a rare genetic condition in which a female is partly or completely missing an X chromosome. Signs and symptoms vary among those affected. In fetuses that survive at birth and without congenital malformations, the prognosis is usually positive, but it has high lethality in utero, especially in the first trimester of pregnancy. We report a case of monosomy X detected during a prenatal diagnosis for beta thalassemia on coelomic fluid (CF) at the VIII week of gestation. Beta globin gene analysis, whole genome amplification (WGA), quantitative fluorescent PCR and array comparative genomic hybridization (array-CGH) were performed on DNA extracted from CF. A monoallelic pattern of all Short Tandem Repeats mapped on the X chromosome was found and array-CGH performed on WGA from a few fetal erythroblasts confirmed monosomy X. This report underlines the importance of an early prenatal diagnosis and the countless potentialities of array-CGH that could make definition of molecular karyotype possible from a few fetal cells, unlike conventional cytogenetic techniques that require a greater cellular content. This is the first report of a molecular karyotype obtained from two cells selected by micromanipulation of CF and defined at such an early gestational age.

Chromosomal rearrangements and the first indication of an ♀X1 X1 X2 X2 /♂X1 X2 Y sex chromosome system in Rineloricaria fishes (Teleostei: Siluriformes).

Rineloricaria is the most diverse genus within the freshwater fish subfamily Loricariinae, and it is widely distributed in the Neotropical region. Despite limited cytogenetic data, records from southern and south-eastern Brazil suggest a high rate of chromosomal rearrangements in this genus, mirrored in remarkable inter- and intraspecific karyotype variability. In the present work, we investigated the karyotype features of Rineloricaria teffeana, an endemic representative from northern Brazil, using both conventional and molecular cytogenetic techniques. We revealed different diploid chromosome numbers (2n) between sexes (33♂/34♀), which suggests the presence of an ♀X1 X1 X2 X2 /♂X1 X2 Y multiple sex chromosome system. The male-limited Y chromosome was the largest and the only biarmed element in the karyotype, implying Y-autosome fusion as the most probable mechanism behind its origination. C-banding revealed low amounts of constitutive heterochromatin, mostly confined to the (peri)centromeric regions of most chromosomes (including the X2 and the Y) but also occupying the distal regions of a few chromosomal pairs. The chromosomal localization of the 18S ribosomal DNA (rDNA) clusters revealed a single site on chromosome pair 4, which was adjacent to the 5S rDNA cluster. Additional 5S rDNA loci were present on the autosome pair 8, X1 chromosome, and in the presumed fusion point on the Y chromosome. The probe for telomeric repeat motif (TTAGGG)n revealed signals of variable intensities at the ends of all chromosomes except for the Y chromosome, where no detectable signals were evidenced. Male-to-female comparative genomic hybridization revealed no sex-specific or sex-biased repetitive DNA accumulations, suggesting a presumably low level of neo-Y chromosome differentiation. We provide evidence that rDNA sites might have played a role in the formation of this putative multiple sex chromosome system and that chromosome fusions originate through different mechanisms among different Rineloricaria species.

Unexpectedly High Prevalence of iAMP21 in Children with Acute Lymphoblastic Leukemia in Mexico: A Report from the "Mexico in Alliance with St. Jude” (MAS) Collaborative Group

Keywords: acute lymphoblastic leukemia, intra-amplification of chromosome 21, genetic characterization. Mexico in Alliance with St. Jude (MAS) has carried out a multi-center collaboration for children with acute lymphoblastic leukemia (ALL) in Mexico since 2019. The "Bridge Project” has granted access to diagnostic tests that allow genetic characterization of children with ALL in participating centers. The Molecular Genetics Laboratory of Hospital Infantil Teleton de Oncologia (HITO) serves as the referral laboratory. 253 newly diagnosed ALL patients from 5 hospitals in Mexico have utilized a comprehensive diagnostic panel that includes cytogenetic and molecular tests to identify relevant abnormalities. iAMP21 is recognized by the 2017 World Health Organization (WHO) Classification of Tumors of Hematopoietic and Lymphoid Tissues as a characteristic genetic alteration of B-lineage Leukemia/Lymphoma, with a reported incidence of up to 2-5%. It involves amplification of the RUNX1 gene and/or duplication of chromosome 21 dup(21q), and defines a relatively new cytogenetic subgroup in B-lineage ALL with poor prognosis, derived from the genetic instability of chromosome 21.The heterogeneity of iAMP21 contributes to the difficulty in its detection with the sole use of conventional cytogenetic techniques, rendering Fluorescent In Situ Hybridization (FISH) as a better strategy for the distinction between iAMP21 (amplification in tandem) and the sporadic gain of copies of the RUNX1 gene. METHODS: We performed a comprehensive diagnostic panel for 253 patients with ALL; the FISH B-cell lymphoid panel included (KMT2A, ETV6 (TEL)/RUNX1 (AML1), BCR/ ABL, E2A/(TCF3)/(PBX1) and the T-cell lymphoid panel included (MLL, BCR / ABL, E2A / (TCF3) / (PBX1), TLX1, TLX3, CDKN2A and TRA / D). Diagnosis of iAMP21 was made using the interphase FISH technique with the LSI ETV6/RUNX1 (Vysis®) double color double fusion probe (Abbott Molecular®, Ill), and Cytocell probe (OGT Company®, NY). A finding of ≥ 5 RUNX1 gene signals in interphase FISH and/or more than 3 signals within chromosome 21 was considered positive for the identification of iAMP21. Samples were processed according to the specifications to the AGT Cytogenetics Laboratory Manual. FISH analysis was performed by analyzing 200 interphase cells. When ETV6/ RUNX1 probes are used, samples of patients carrying iAMP21 usually show two normal copies of the ETV6 signal and multiple RUNX1 signals (three or more additional signals) and are negative for the ETV6-RUNX1 fusion gene. RESULTS: Among 253 patients with ALL, 233 cases were of lineage B (92%) and 20 (8%) were of lineage T. FISH was reported negative in 57 (23%) and positive in 185 (73%) cases, 11 results were not available (4.3%). We detected iAMP21 in 28 (11%); these cases were classified as high risk. We also report t(12;21) in 41 (16%), MLL gene disruption t(4;11) in 10 (4%), t(1;19) in 14 (6%), and t(9;22) in 7 (3%); 75 (30%) patients had nonspecific genetic gains. The T lineage showed CDKN2A del(9)(p21) in 6 (2.5%) and TRA/D(14)(q11.2) rearrangement in 4 (1.7%) cases. CONCLUSION: Our experience shows that FISH analysis with the ETV6/RUNX1 probe is useful for identifying iAMP21, a chromosomal abnormality with prognostic significance. Genetic risk factors in the Hispanic population that adversely impact survival in Latin America are not yet fully identified. The Molecular genetic analysis and the fluorescence in situ hybridization (FISH) technique are the basic methods used to detect the presence of the most common genetic abnormalities, the presence or absence of which has an impact on the patient's classification into the appropriate risk group. Our findings from this cohort point to an increased prevalence of iAMP21 in ALL patients in Mexico. We will soon incorporate gene sequencing to the diagnostic panel and improve the characterization of these patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Overlapping Interstitial Deletions of the Region 9q22.33 to 9q33.3 of Three Patients Allow Pinpointing Candidate Genes for Epilepsy and Cleft Lip and Palate

Introduction: Patients carrying interstitial deletions of the long arm of chromosome 9 show similar features. These phenotypes are often characterized by developmental delay, intellectual disability, short stature, and dysmorphism. Previously reported deletions differ in size and location spanning from 9q21 to 9q34 and were mostly detected by conventional cytogenetic techniques. Methods: Based on clinical features suggesting primarily chromosomal diseases, aCGH analysis was indicated. We report on de novo overlapping interstitial 9q deletions in 3 unrelated individuals presenting neurodevelopmental disorder and multiple congenital anomalies. Results: An 8.03-Mb (90 genes), a 15.71-Mb (193 genes), and a 15.81-Mb (203 genes) deletion were identified in 9q affecting 9q22.33q33.3. The overlapping region was 1.50 Mb, including 2 dosage-sensitive genes, namely EPB41L4B (OMIM #610340) and SVEP1 (OMIM #611691). These genes are thought to be involved in cellular adhesion, migration, and motility. The non-overlapping regions contain 24 dosage-sensitive genes. Conclusion: Besides the frequently described symptoms (developmental delay, intellectual disability, skeletal abnormalities, short stature, and dysmorphic facial features) shared by the patients with interstitial deletions of chromosome 9q reported thus far, two of our patients showed distinct forms of epilepsy, which were successfully treated, and one had a bilateral cleft lip and palate. Possible candidate genes for epilepsy and cleft lip and palate are discussed.

P504: CLINICAL MUTATIONAL ANALYSIS BY NEXT-GENERATION SEQUENCING AND REAL-LIFE VALIDATION OF THE REVISED 2017 EUROPEAN LEUKEMIANET GENETIC RISK STRATIFICATION IN AML PATIENTS

Background: Recently, a census of mutated genes in AML has been described but their value in clinical practice is not fully elucidated. The revised 2017 European LeukemiaNet (ELN) recommendations for genetic risk stratification of AML have been widely adopted, but have not yet been validated in large cohorts of AML patients in real life. Aims: The objective of this work is to analyze the mutations detected by Next Generation Sequencing (NGS) and to study whether the application of ELN 2017 scale improves prognostic risk stratification with respect to ELN 2010 and Medical Research Council (MRC). Methods: We included 112 adult AML patients diagnosed in our center between Jun2017 and Dec2021 and who were studied at diagnostic using the spanish PLATFOLMA PETHEMA. The prognostic risk was established according to MRC, ELN2010 and ELN2017 classification. Baseline demographic, disease characteristics, treatment procedures and mutations by functional groupsare summarized in Table 1 NPM1 and FLT3-ITD were determined by melting curve analysis and standard PCR-EC technique according to Thiede et al (Blood 2002) in ABI 3130 Analyzer (Thermofisher). For NGS, the commercial panel Myeloid SolutionTM (Sophia Genetics) KAPA Kit amplification libraries and sequencing on ILUMINA Myseq platform were used. Variant analysis was performed using DDM software (Sophia Genetics). Results: The majority of the patients (97.1%) had at least one mutation at diagnosis detected by NGS. The median number of mutations was 2.36 (0-6). Grouped by functional groups, the most frequent were those related to DNA methylation (44.6 %) and signaling/kinase pathways (37.5%). The most prevalent were FLT3 (29 %), IDH1/IDH2 (27%) and TP 53 (19.6%) followed by NPM1 and RUNX-1 (17%). Patients older than 60 years, presented higher percentage of unfavorable ASXL1 (18.6%), RUNX1 (20%) and TP53 (25.7%) mutations with respect to younger (4.8%, 11.9% and 9.5 %) being these differences statistically significant in ASXL 1 and TP 53 (χ2 p=0.044 and p=0.047 respectively). NPM1 (28.6%) and FLT3 (40.5%) mutations were significantly more frequent in younger patients (χ2 p=0.017 and p=0.013 respectively), than in >60 years (10% and 17.1%, respectively). Re-stratifying according to ELN 2017, the 53% of patients categorized within the intermediate risk group according to MRC change prognostic group: 28.9% became redefined as unfavorable risk and 24.1% as favorable. In the overall series the overall survival analysis shows statistically significant differences taking into account either ELN 2017 or ELN 2010 and MRC (T.logrank p=0.003, p=0.018 and p=0.012, respectively). However, according to ELN 2017 there are greater differences between intermediate and unfavorable groups than in the other classifications. Statistically significant differences in overall survival according to ELN 2017 (T.logrank p=0.028) are also found in patients receiving intensive treatment. The estimated overall survival at two years is 72.%, 52.1% and 46.8% in the favorable, intermediate and unfavorable group, respectively. Image:Summary/Conclusion: - NGS proves its usefulness by detecting more clinically relevant alterations than conventional cytogenetic techniques and PCR, and stratifies a larger group of patients as favorable and unfavorable. - Our results validate the prognostic significance of the ELN2017 classification in real life, both in the overall series and in candidates for intensive QT. - ELN 2017 establishes greater survival differences between the intermediate and unfavorable group than ELN 2010 and MRC redefining the intermediate group.

Classic and molecular cytogenetic analysis unveils different chromosome rearrangements shaping the karyotype ofMonobia angulosaSaussure, 1852 (Hymenoptera: Vespidae: Eumeninae)

AbstractCytogenetic molecular studies involving hymenopterans have improved our knowledge about the composition, organization and evolution of the genomes of these insects. However, few cytogenetic studies have been performed in solitary wasps Eumeninae, which represents the most diverse subfamily of Vespidae. In this study, we describe the karyotype of the wasp Monobia angulosa using conventional and molecular cytogenetic techniques, in order to contribute to the understanding of chromosomal variation in this solitary wasp. The results indicated an odd chromosome number of 2n = 27 in females and n = 14 in males. The heterochromatin was located in centromeric/pericentromeric regions, and also in short arms in females and males. Chromomycin A3 staining revealed four and two bright interstitial bands in females and males, respectively. One of these marks corresponded to 18S rDNA clusters in both females and males. The microsatellite (GA)15 was located exclusively in the euchromatic regions in females and males. These results allowed us to suggest the occurrence of different chromosomal rearrangements, such as duplication/deletion of heterochromatic and euchromatic segments due to unequal crossing-over and Robertsonian rearrangements, to explain the origin of the chromosomal variations detected in the karyotype of this species. The few molecular cytogenetic studies already performed with Eumeninae wasps have revealed extraordinary karyotypic plasticity in this insect group.

Cytogenetic Analyses Detect Cryptic Diversity in Megaderma spasma from Malaysia

As many as 17 subspecies are currently recognized for the lesser false vampire, Megaderma spasma along its wide distributional range, from India to Southeast Asia. Cytogenetic studies have been so far restricted to specimens from only four geographical regions, namely Malaysia, Thailand, China and the Philippines. We examined the karyotypes of M. spasma medium from Peninsular Malaysia and M. s. trifolium from Malaysian Borneo with conventional and molecular cytogenetic techniques, using whole chromosome painting probes from the vespertilionid Myotis myotis and the hipposiderid Aselliscus stoliczkanus. Both Megaderma subspecies showed the same diploid chromosome number, 2n = 38, but differed concerning interstitial heterochromatic segments and number and shape of heterochromatic B chromosomes. Comparison with published data revealed that the Bornean specimens' karyotype best resembled the chromosomal set of the Chinese specimen. In contrast, a single male specimen from Malaysian Borneo showed a different karyotype (2n = 40) without B chromosomes and interstitial heterochromatin, indicating that it may represent a cryptic, yet unknown Megaderma species.

Correlation of Maternal Age and Chromosomal Abnormality in Products of Conception- A Single Centric Study

Purpose: The purpose of this study is to find out the types and incidence rate of chromosomal abnormalities and the relationship between maternal age and chromosomal abnormality in products of conception by retrospective analysis. Method: Karyotype study using standard GTG banding and FISH study for aneuploidy detection was done from products of conception samples. Results: A total of 513 cases of products of conception were studied retrospectively. 98 cases were studied by conventional cytogenetic technique and 415 cases were studied by a FISH method. The chromosomal abnormality was observed in 97 cases (18.91%). Trisomy was found to be a major chromosomal abnormality amongst the cases studied, followed by triploidy and monosomy. A higher incidence of chromosomal abnormality was found in women with advanced maternal age as compared to the maternal age less than 35 years.

CHROMOSOMAL POLYMORPHISM IN BULGARIAN PATIENTS WITH REPRODUCTIVE PROBLEMS – ONE GENETIC CENTRE EXPERIENCE

Chromosomal polymorphism is described as normal variants at chromosomal regions with no impact on the phenotype but a possible correlation to infertility and recurrent spontaneous abortions. The aim of this study was to evaluate the effect of the chromosomal polymorphisms involved in families with reproductive failures in the Bulgarian population. Material and methods: A total of 1733 patients with unexplained reproductive failures who visited the Laboratory of Medical Genetics – Varna, Bulgaria, (2004 - 2019) were investigated by conventional cytogenetic analysis GTG and CBG differential banding techniques and analyzed at the resolution 400-550 GTG bands. Results: Chromosomal polymorphisms were found in 173 infertile patients (9,98%). The sex distribution was 6,52% males and 3,46% females. The most frequent finding was inv(9)(qh) (23,7%). The other chromosomal variants, which were found, consisted: 9qh+/- variants (15,1%); polymorphisms on the short arms of the acrocentric chromosomes (21,4%); 16qh+ (12,7%) and 1qh+ (6,9%). Y chromosome polymorphism was found in 27,4% of the males with polymorphisms. Two rare cases of polymorphism involving the centromere regions - 19qcenh+ and 20pcenh+ were also found. Conclusion: There is growing evidence that polymorphisms may have a clinical impact on fertility and could take part in the etiology of RF. In this study, we found a significantly high percentage of polymorphisms (9,98%) among the tested patients, and they were more common among males. The statistical significance of increased incidence of chromosome variations found in our study emphasizes the need for routine evaluation of their role in families with RF in our country.

Whole-genome analysis of a putative rare and complex interchromosomal reciprocal insertion: thorough investigations for a straightforward interpretation

Research questionShould whole-genome investigations be considered systematically before a complex chromosomal abnormality preimplantation genetic testing for structural chromosomal rearrangements (PGT-SR) management is carried out using conventional cytogenetic techniques? DesignA male carrying a putative rare interchromosomal reciprocal insertion (IRI) 46,XY,ins(14;?)(q11;?).ish der(14)ins(14;22)(q11.2;q11.2q11.2)(xcp14+,xcp22+,N25+,3’TRA/D+),der(22)ins(22;14)(q11.2;q11.2q11.2)(xcp22+,xcp14+,N25-,5’TRA/D+), and his partner were referred to our centre for preimplantation genetic testing analysis after three spontaneous miscarriages. Whole-genome sequencing was used to distinguish between the proposed IRI and an alternative explanation of reciprocal translocation. Fluorescence in-situ hybridization was used to detect all chromosome segments involved in this chromosomal rearrangement, to identify transferable normal and balanced embryos. ResultsWhole-genome sequencing allowed the determination of the number of chromosomal breakpoints involved in chromosomal rearrangement between chromosomes 14 and 22. Finally, only two breakpoints were identified instead of four in IRI rearrangements, which suggests a reciprocal translocation rearrangement. A probe strategy was established to highlight all chromosomal imbalances, whether IRI or reciprocal translocation, and preimplantation genetic testing cycles were achieved. ConclusionConventional cytogenetic techniques are not capable of identifying all complex chromosomal rearrangements, especially those involving centromeric regions and short arms of acrocentric chromosomes. The advent of new sequencing technologies has allowed for a better appreciation of genome complexity. In this study, whole-genome analysis provided additional information to explain the occurrence of genomic events and confirmed that the initial diagnosis of IRI identified by conventional cytogenetic techniques was, in fact, a simple reciprocal translocation. A reliable PGT-SR strategy was proposed for this couple to achieve their parental project.

O-237 A non-invasive approach for aneuploidy analysis in clinical miscarriages

Abstract Study question Is maternal cell-free DNA (cfDNA) testing a feasible alternative to the analysis of the product of conception (POC) in clinical miscarriages? Summary answer This study demonstrates that genome-wide cfDNA testing in the maternal bloodstream constitutes a reliable tool to analyse chromosome aneuploidies in clinical miscarriages. What is known already It is well established that 50-70% of clinical miscarriages are caused by numerical chromosomal anomalies (aneuploidies), mostly trisomies. To date, conventional cytogenetic and advanced molecular techniques are used for the analysis of POC to identify the genetic cause of miscarriage, providing valuable information for genetic counselling. However, both approaches are based in the direct analysis of the abortive tissue, which entails several limitations due to the risk of culture failure and/or maternal cell contamination. To solve these drawbacks, maternal cfDNA testing emerges as a promising alternative due to the accumulated evidence. Study design, size, duration This was a retrospective study conducted in a reference genetic laboratory from January to December 2020. Before carrying out the foetal tissues collection that precludes the POC analysis, a blood sample was drawn to evaluate possible aneuploidies by cfDNA testing. Using NGS+STR POC results as the gold standard, results derived from both studies were compared to assess the percentage of concordance and the cases of non-informativeness (foetal fraction (FF) <2%), false positives, and false negatives. Participants/materials, setting, methods A total of 12 cases were included in the study. cfDNA testing in the mother’s blood was performed by using Illumina’s technology platform. Genetic testing for POC was done using an NGS technology (Thermo Fisher Scientific, USA) for 24 chromosome aneuploidy screening. Short-tandem repeat (STR) analysis allowed us to detect or rule out maternal cell contamination (MCC) and some types of polyploidies. Main results and the role of chance The non-informative rate for both analysis techniques was 9.1% (1 out of 12 cases: 1 low FF for cfDNA testing and maternal cell contamination for POC analysis). The median cfDNA FF was 9.0%. Using the molecular POC analysis as gold standard, the concordance rate between both studies was 90.0% (9 out of 10 cases;1 monosomy X, 1 trisomy (T) 21, 1 T22, 1 T11 and 5 patients with no alteration detected). No mosaics or structural rearrangements were identified by either of the two analysis techniques. The only discordant result was a case in which cytogenetics of POCs identified a triploidy. This discordancy is expected since triploidies are outside the scope of cfDNA testing. Also, foetal sex was correctly assigned in all informative cases. The sensibility and specificity of the study were estimated at 80.0 (4/5) and 100.0% (6/6), respectively. Statistics analysis suggested that no significant difference was found between both techniques regarding the aneuploidy detection ability (P=0.5). These promising results indicate that genome-wide cfDNA-based screening provides a non-invasive approach for determining whether foetal aneuploidy could explain the loss in patients experiencing early o recurrent pregnancy loss (RPL). Limitations, reasons for caution The sample size prevents drawing more significant conclusions regarding the diagnosis power similarity between both testing techniques. Therefore, a larger cohort will be essential to improve confirm the cfDNA testing performance. Current cfDNA testing technology fails in polyploidy identification, which is a potential cause of pregnancy loss. Wider implications of the findings CfDNA testing could be an alternative to POC analysis in clinical miscarriage. If optimized, cfDNA testing could be used contingently with the molecular POC analysis in cases where maternal cell contamination is present. As a result, the overall success rate in the POC program could be substantially improved. Trial registration number NA

Cytogenetic findings of ectopic endometriotic tissue in women with endometriosis and review of the literature

ObjectiveTo determine chromosome and gene alterations in ectopic endometrial (EM) tissue which may be implicated in the clinical course or the progression of endometriosis and to review the literature concerning the cytogenetic findings of women with endometriosis. Study design15 women who underwent laparoscopic endometriosis surgery at the Athens Genesis Clinic were enrolled in the study. Ectopic endometrial tissue was surgically removed and further analyzed by conventional and molecular cytogenetic techniques. Fluoresent in situ hibridization (FISH) with probes for p53, ATM, MYC, MLL1 and IGH genes, the centromeres of chromosomes 7 and 8 and 7q22/7q31 chromosomal regions was carried out. ResultsKaryotypic analysis revealed no clonal chromosomal abnormalities. However, an increased frequency of polyploidy (55.6%) and sporadic chromosomal abnormalities (40.0%) concerning chromosomes 9, 11, 17 and X were noticed involving mainly deletions, trisomies or monosomies. FISH analysis showed IGH gene rearrangements in 54% of the EM cases and MLL gene rearrangements in 73% of the examined samples. Normal hybridization patterns were observed for p53, ATM and MYC. The increased frequency of polyploidy shown by conventional karyotyping was also confirmed by FISH. ConclusionPolyploidy, sporadic chromosomal abnormalities, as well as IGH and MLL gene rearrangements, may provoke genetic instability and play a potential role in the development of endometriosis. IGH and MLL gene rearrangements indicate a genetic relation between endometriosis and carcinogenesis. Confirmation of the above gene rearrangements in a large series of women may allow the determination of their possible involvement in the pathogenesis of this complex disease and their possible contribution in the early identification of women in danger for malignant transformation.