Analysis Of Aneuploidy Research Articles

Study of the feasibility of polar body transfer combined with preimplantation genetic testing for blocking the intergenerational transmission of mitochondrial genetic diseases

To assess the feasibility of first polar body transfer (PB1T) combined with preimplantation mitochondrial genetic testing for blocking the transmission of a pathogenic mitochondrial DNA 8993T>G mutation. A Chinese family affected with Leigh syndrome which had attended the Reproductive Medicine Centre of the First Affiliated Hospital of Anhui Medical University in September 2021 was selected as the study subject. Controlled ovarian hyperstimulation was carried out for the proband after completing the detection of the mitochondrial DNA 8993T>G mutation load among the pedigree members. Mature MII oocytes were inseminated by intracytoplasmic sperm injection (ICSI), cultured in vitro for 5 to 6 days to the blastocyst stage, and trophoblastocytes were obtained by microbiopsy. Mitochondrial DNA testing (PGT-MT) and chromosomal aneuploidy (PGT-A) analyses were carried out after whole-genome amplification, and the embryos with zero mutation load were selected for transfer. Amniotic fluid and umbilical cord blood samples were collected during middle pregnancy and after birth respectively for mitochondrial DNA testing to verify the reliability of embryo screening. As an attempt, PB1 with good morphology of MII oocytes was selected for transfer into the enucleated oocytoplasm from healthy donors, followed by ICSI fertilization, blastocyst culture and PGT of embryos using the same procedure. This study has been approved by the Ethics Committee of the First Affiliated Hospital of Anhui Medical University (No. 2021zhyx-B12). An antagonist protocol was used for ovarian stimulation, and a total of 19 oocytes were obtained, of which 14 MII were fertilized by ICSI, and 2 had developed into blastocysts. PGT-MT was carried out on biopsied trophoblastocytes, in which the mitochondrial DNA 8993T>G mutation load was not detected in one embryo, the other was 100% mutated, and the mutation loads of the remaining unfertilized eggs and developmentally arrested embryos ranged from 0% ~ 100%, presenting a clear biased distribution. With fully informed consent, one PGT-MT zero mutation load blastocyst was transferred and clinical pregnancy was achieved. Mitochondrial DNA and chromosomal testing of amniotic fluid cells during middle pregnancy had revealed no abnormalities. The proband had delivered a healthy boy through Caesarean section at 39+5 weeks of gestation, and no mutation was detected in the cord blood sample. Five well-formed PBs from 14 eggs were selected for PB1 transfer, followed by ICSI and culture, and two of the reconstituted embryos had formed blastocysts, with none of the above mutations detected in the biopsied samples. The PGT-MT technology can help families affected with mitochondrial diseases to have healthy offspring. PB1 transfer in combination with ICSI and PGT-MT holds the promise of turning waste into treasure and providing an alternative means of fertility for such families.

Inference of chromosome selection parameters and missegregation rate in cancer from DNA-sequencing data

Aneuploidy is frequently observed in cancers and has been linked to poor patient outcome. Analysis of aneuploidy in DNA-sequencing (DNA-seq) data necessitates untangling the effects of the Copy Number Aberration (CNA) occurrence rates and the selection coefficients that act upon the resulting karyotypes. We introduce a parameter inference algorithm that takes advantage of both bulk and single-cell DNA-seq cohorts. The method is based on Approximate Bayesian Computation (ABC) and utilizes CINner, our recently introduced simulation algorithm of chromosomal instability in cancer. We examine three groups of statistics to summarize the data in the ABC routine: (A) Copy Number-based measures, (B) phylogeny tip statistics, and (C) phylogeny balance indices. Using these statistics, our method can recover both the CNA probabilities and selection parameters from ground truth data, and performs well even for data cohorts of relatively small sizes. We find that only statistics in groups A and C are well-suited for identifying CNA probabilities, and only group A carries the signals for estimating selection parameters. Moreover, the low number of CNA events at large scale compared to cell counts in single-cell samples means that statistics in group B cannot be estimated accurately using phylogeny reconstruction algorithms at the chromosome level. As data from both bulk and single-cell DNA-sequencing techniques becomes increasingly available, our inference framework promises to facilitate the analysis of distinct cancer types, differentiation between selection and neutral drift, and prediction of cancer clonal dynamics.

Cell-Free DNA Analysis of Fetal Aneuploidies in Early Pregnancy Loss.

Background: Products of conception samples are often collected and analyzed to try to determine the cause of an early pregnancy loss. However, sample collection may not always be possible, and maternal cell contamination and culture failure can affect the analysis. Cell-free DNA-based analysis of a blood sample could be used as an alternative method in early pregnancy loss cases to detect if aneuploidies were present in the fetus. Methods: In this prospective study, blood samples from early pregnancy loss patients were analyzed for the presence of fetal aneuploidies using a modified version of a noninvasive prenatal testing assay for cell-free DNA analysis. Results from cell-free DNA analysis were compared against the gold standard, microarray analysis of products of conception samples. This study was registered with ClinicalTrials.gov, identifier: NCT04935138. Results: Of the 76 patient samples included in the final study cohort, 11 were excluded from performance calculations. The 65 patient samples included in the final analysis included 49 with an abnormal microarray result and 16 with a normal microarray result. Based on results from these 65 samples, the study found that genome-wide cell-free DNA analysis had a sensitivity of 73.5% with a specificity of 100% for the detection of fetal aneuploidies in early pregnancy loss cases. Conclusions: This prospective study provides further support for the utility of cell-free DNA analysis in detecting fetal aneuploidies in early pregnancy loss cases. This approach could allow for a noninvasive method of investigating the etiology of miscarriages to be made available clinically.

P-563 Improved diagnosis in PGT-A samples with intermediate sex chromosomes copy number changes by adding ploidy and contamination analysis

Abstract Study question Does triple analysis of aneuploidy, ploidy and contamination improve the diagnosis in samples with intermediate copy number changes for the X and the Y chromosomes? Summary answer PGT-A with additional ploidy and contamination analysis improves the diagnosis of samples with intermediate sex chromosomes copy number changes, reducing non-informativity and the re-biopsy need. What is known already Next Generation Sequencing (NGS) in Preimplantation Genetic Testing for Aneuploidies (PGT-A) identifies chromosomal aneuploidies in trophectoderm (TE) biopsies. However, diagnosis limitations exist when the TE biopsy displays intermediate copy number changes for the X and the Y chromosomes, observed in ∼0.3% of biopsies. Few explanations are plausible, including mosaicism for the sex chromosomes, presence of exogenous DNA contamination or triploidy. A second TE biopsy (re-biopsy) could be recommended to obtain a conclusive result. However, additional Single Nucleotide Polymorphism (SNP) analysis to determine the ploidy status of the embryo and the presence of contamination in the biopsy can be an alternative. Study design, size, duration In this retrospective study, the impact on the diagnosis of SNPs analysis with a target panel was evaluated in PGT-A samples showing intermediate copy number changes for the X and the Y chromosomes. A total of 21 TE biopsies from January to December 2023 were included in the study. Participants/materials, setting, methods The TE biopsies were analysed using NGS with a proprietary protocol for library preparation, Ion Chef and Ion S5 System instruments for sequencing and a proprietary bioinformatics pipeline (v2.0) for 24-chromosomes aneuploidy testing. A re-biopsy was analysed in 8 embryos using the same protocol. Eighteen original biopsies were retrospectively evaluated for ploidy and contamination using an Ion AmpliSeq Custom Panel including SNPs (Thermo Fisher Scientific, USA) and a proprietary algorithm (v1.0) for data analysis. Main results and the role of chance The 21 TE biopsies displaying intermediate copy number changes for the X and the Y chromosomes were initially diagnosed as non-informative and candidates for re-biopsy to rescue diagnosis. A total of 8 embryos were re-biopsied (38.1%): 6 re-biopsies (75.0%) showed the same intermediate sex chromosomes copy number changes suggesting a triploid status of the embryo, 1 re-biopsy (12.5%) showed trisomy 22 suggesting DNA contamination in the original biopsy and, 1 re-biopsy (12.5%) displayed a mosaic monosomy X/XY suggesting a diploid-mosaic status of the embryo. In 18 original TE biopsies (85.7%), an additional ploidy and contamination analysis was done: 10 samples were triploid (55.6%), 6 samples showed DNA contamination (33.3%) and 2 samples were diploid (11.1%). In 5 embryos, the re-biopsy with the aneuploidy testing had been done: (i) in 4 triploid embryos the re-biopsies showed the same intermediate copy number changes for the sex chromosomes than the original biopsy, confirming the triploid status of the embryo; (ii) in 1 diploid embryo the re-biopsy showed a mosaic monosomy X/XY, confirming the diploid status and the sex chromosome mosaicism of the embryo. From the 21 embryos initially non-informative, only the 6 contaminated ones remained non-informative and candidates for re-biopsy (33.3%). Limitations, reasons for caution The limited number of samples with both analysis, ploidy/contamination by SNPs in the original sample and aneuploidy by NGS in the re-biopsy precluded to drawn stronger conclusions. This double-check would reinforce the benefit of doing additional ploidy/contamination analysis in these specific cases. Wider implications of the findings A high incidence of samples with intermediate sex chromosomes copy number are triploid, some have exogenous DNA contamination, and few are real mosaics for the sex chromosomes. Additional ploidy and contamination analysis could improve the PGT-A diagnosis and decrease mosaicism and non-informativity rates, reducing the embryos that would need re-biopsy. Trial registration number Not applicable

P-107 Sperm DNA fragmentation impacts embryonic developmental potential but is not associated with PGT-A outcomes

Abstract Study question Does sperm DNA Fragmentation Index (DFI) affect embryonic development and influence Preimplantation Genetic Testing for Aneuploidy (PGT-A) outcomes in IVF? Summary answer DFI adversely affects early embryonic development, diminishing blastocyst potential. Nonetheless, PGT-A outcomes are unaffected, underscoring the importance of selecting optimal sperm for enhanced IVF results. What is known already Several major factors are thought to cause DFI. The relationship between sperm DFI and IVF results remains debated. Study design, size, duration This study was conducted from January 2018 to March 2023, included 56 married couples undergoing IVF after performing a sperm DFI test. The DFI was assessed at the first semen examination and categorized into three groups: low (≤15%), moderate (15-30%), and high (≥30%). Participants/materials, setting, methods Intracytoplasmic sperm injection (ICSI) was performed on 1006 mature oocytes, followed by blastocyst culture. A total of 278 blastocysts meeting freezing criteria were vitrified. Trophectoderm biopsies from 216 blastocysts underwent Next-Generation Sequencing for aneuploidy analysis. Statistical analysis utilized the Cochran-Armitage test to compare outcomes among the DFI groups. Main results and the role of chance The average age of the husbands and wives who underwent IVF after the DFI examination was 42.3±4.2 and 41.4±2.4 years old. Normal fertility rates after ICSI in low, moderate, and high DFI were 85.5%, 84.5%, and 83.1%, with no significant difference. Similarly, the blastocyst freezing rates were 35.4%, 26.3%, and 29.6%, and tended to decrease as the DFI value increased (p < 0.05). However, the euploid rates for PGT-A were 22.4%, 16.3%, and 18.2%. There were no statistically significant differences between the DFI groups in terms of euploidy. Limitations, reasons for caution Cases declining ICSI due to patient preference or historical medical reasons were excluded from this study. Wider implications of the findings This suggests that sperm DNA imperfections have a negative impact on the developmental process during the early stages of division, but during late stages of division, the ability to repair DNA works to differentiate into blastocysts with normal developmental potential. Trial registration number not applicable

P-136 Non-invasive PGT (niPGT) using spent culture medium: Relationship between time lapse embryo dynamics and accuracy of niPGT analysis

Abstract Study question Do differences in the morphological characteristics of embryos or the dynamics of the developmental process affect the results of niPGT analysis? Summary answer Embryos with blastomeres that were excluded at compaction showed reduced accuracy of niPGT analysis, but other measured morphological characteristics had no impact. What is known already The PGT-A test, is invasive and requires training to be competent at the technique, aswell as the need for specialized equipment and consumables. In recent years, non-invasive PGT-A (niPGT-A), which analyzes Cell-Free DNA released from cultured embryos, has been attracting attention. Regarding the analysis accuracy of niPGT-A, there are reports that it is equivalent to or even superior to conventional PGT-A. However, at present, it is not clear how methodological differences or embryo dynamics impact results. Study design, size, duration From August 2021 to February 2022, 284 pronuclear-stage frozen embryos (with consent for research use), were thawed and cultured. They were individually cultured for at least 40 hours after Day 4. For the 150 embryos that reached the blastocyst stage, culture medium and the blastocysts were collected and subjected to chromosome aneuploidy analysis by NGS. For the 138 blastocyst with a result, the concordance rate was calculated with that obtained from the culture medium samples. Participants/materials, setting, methods The embryos were individually cultured in a single step medium using a 10 μl droplet from Day 4. The entire culture period was recorded in a time-lapse incubator. The concordance rate for all chromosomes between culture medium sample and the blastocyst was compared to recorded embryo dynamics, e.g. presence or absence of cumulus cell attachment, sperm attachment, fragmentation, blastomeres that excluded at compaction, shrinkage, and hatching. Chi-square test was used to compare the concordance rates. Main results and the role of chance The overall concordance rate for all chromosomes between the culture medium and the blastocysts samples was 46.4%(64/138). In the blastocysts where there were cumulus cells attached or not it was 43.6% (17/39) vs 47.5% (47/99) respectively, cases where there was still a sperm attached or not it was 53.1% (17/32) vs 44.3% (47/106) resepctively and in blastocysts where there had been fragmentation or no fragmenattion it was 46.9%(38/81) vs 45.6％(26/57) respectively. In cases where shrinkage of the blastocyst had been observed vs no shrinkage the respective concordance rates were 44.9% (48/107) vs 51.6% (16/31), whilst in cases where the blastocyst had hatched or not it was 40.6% (13/32) vs 48.1% (51/106) respectively.For the blastocysts where the blastomeres had been excluded at compaction or not it was 35.6％(31/87) vs 64.7% (33/51) respectively.Significant differences were only identified in cases with blastomere exclusion or no exclusion at compaction (P < 0.01). Limitations, reasons for caution In this study, the culture was continued to day 6 regardless of morphology of the embryo on day 5, which differs from the usual clinical culture process. Wider implications of the findings These results are useful in that they may aid in recognising which morphological features of embryos may impact the results obtained from niPGT and hence its reliability for clinical application. The blastomeres that excluded at compaction are clearly important for improving the accuracy of the niPGT analysis in the future. Trial registration number None

Preimplantation genetic testing for a Chinese pedigree affected with Rett syndrome

To carry out preimplantation genetic testing (PGT) for a Chinese pedigree affected with Rett syndrome (RTT). A pedigree affected with RTT who had presented at the First Hospital of Jilin University on June 4, 2021 was selected as the study subject. Variant of the MECP2 gene was analyzed by next generation sequencing (NGS) and Sanger sequencing. Direct sequencing was also used to determine the carrier status for the c.925C>T variant of the MECP2 gene in the blastocysts, and Sanger sequencing was used to validate the results. The MECP2 gene and 168 effective single nucleotide polymorphism (SNP) loci within 2 Mb ranges up- and downstream of the gene were used to construct a haplotype for analyzing the variant site in the embryos, and embryos without the variant were subjected to the analysis for chromosomal aneuploidies. PGT analysis revealed that five out of seven blastocysts did not harbor the pathogenic variant. The results of aneuploidy analysis indicated that two out of five blastocysts without the variant were euploid. Following genetic counselling, the couple had opted to transplant the optimal blastocyst. Following clinical pregnancy, prenatal diagnosis showed that the fetus has a normal chromosomal karyotype, and the c.925C>T variant was not detected in the amniotic fluid sample. A healthy girl was born by Cesarean section at full term. NGS can attain efficient PGT detection and reduce the risk of disease recurrence in families affected with RTT.

Development of a novel prognostic signature based on single-cell combined bulk RNA analysis in breast cancer.

Breast cancer (BC), a malignant tumor, is a significant cause of death and disability among women globally. Recent research indicates that copy number variation plays a crucial role in tumor development. In this study, we employed the Single-Cell Variational Aneuploidy Analysis (SCEVAN) algorithm to differentiate between malignant and non-malignant cells, aiming to identify genetic signatures with prognostic relevance for predicting patient survival. We analyzed gene expression profiles and associated clinical data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Using the SCEVAN algorithm, we distinguished malignant from non-malignant cells and investigated cellular interactions within the tumor microenvironment (TME). We categorized TCGA samples based on differentially expressed genes (DEGs) between these cell types. Subsequent Kyoto Encyclopedia of Genes and Genomes pathway analysis was conducted. Additionally, we developed polygenic models for the DEGs using least absolute shrinkage and selection operator-penalized Cox regression analysis. To assess the prognostic accuracy of these characteristics, we generated Kaplan-Meier and receiver operating characteristic curves from training and validation datasets. We also monitored the expression variations of prognostic genes across the pseudotime of malignant cells. Patients were divided into high-risk and low-risk groups based on median risk scores to compare their TME and identify potential therapeutic agents. Lastly, polymerase chain reaction was used to validate seven pivotal genes. The SCEVAN algorithm identified distinct malignant and non-malignant cells in GSE180286. Cellchat analysis revealed significantly increased cellular communication, particularly between fibroblasts, endothelial cells and malignant cells. The DEGs were predominantly involved in immune-related pathways. TCGA samples were classified into clusters A and B based on these genes. Cluster A, enriched in immune pathways, was associated with poorer prognosis, whereas cluster B, predominantly involved in circadian rhythm pathways, showed better outcomes. We constructed a 14-gene prognostic signature, validated in a 1:1 internal TCGA cohort and external GEO datasets (GSE42568 and GSE146558). Kaplan-Meier analysis confirmed the prognostic signature's accuracy (p < 0.001). Receiver operating characteristic curve analysis demonstrated the predictive reliability of these prognostic features. Single-cell pseudotime analysis with monocle2 highlighted the distinct expression trends of these genes in malignant cells, underscoring the intratumoral heterogeneity. Furthermore, we explored the differences in TME between high- and low-risk groups and identified 16 significantly correlated drugs. Our findings suggest that the 14-gene prognostic signature could serve as a novel biomarker for forecasting the prognosis of BC patients. Additionally, the immune cells and pathways in different risk groups indicate that immunotherapy may be a crucial component of treatment strategies for BC patients.

DNA image cytometry of bronchial washing as a diagnostic adjunct to radial endobronchial ultrasound-guided sampling of peripheral lung lesions: A single center prospective study.

The objective of this study is to study the adjunct role of combining DNA aneuploidy analysis with radial endobronchial ultrasound (R-EBUS)-guided sampling for diagnosis of peripheral lung lesions (PPLs). A single-center prospective study was conducted in patients undergoing R-EBUS-guided sampling for PPLs. DNA image cytometry (DNA-ICM) was used to analyze DNA aneuploidy in bronchial washing from the bronchial segment of the PPL. Clinical information, R-EBUS data, pathology, DNA-ICM results, and follow-up data were analyzed. Sensitivity, specificity, and predictive values for R-EBUS-guided sampling, DNA-ICM, and the two methods combined were measured. Binary logistic regression was performed to determine influencing factors on diagnostic positivity rate. Receiver operating characteristic (ROC) curve analysis was used to determine the optimal cutoff point for DNA-ICM. A total of 101 patients were enrolled. Sixty-four (63.4%) patients had confirmed malignant tumor, of whom 33 were confirmed by R-EBUS-guided sampling (biopsy and/or bronchial brush and wash cytology), and 31 by surgery or percutaneous lung biopsy. Thirty-seven patients were finally considered to have benign lesions, based on clinical information and 1-year follow-up. The sensitivity for malignant disease was 51.6% by R-EBUS, and specificity was 100%. DNA-ICM had a sensitivity of 67.2% and a specificity of 86.5%. When combining the two methods, sensitivity increased to 78.1% and specificity was 86.5%. Lesion size and whether the R-EBUS probe was located in the lesion were significantly associated with positivity rate of the combined methods. The optimal cutoff point for DNA-ICM was 5c for max DNA content, and 1 for aneuploid cell count (sensitivity 67.2%, specificity 86.5%, accuracy 63.4%). In malignant PPLs, DNA-ICM combined with R-EBUS-guided sampling can improve diagnostic positivity compared with either method alone.

P-644 The mitochondrial DNA copy number in cumulus cells associate with age and AMH level but do not predict implantation potential of embryos

Abstract Study question is there correlation between the mtDNA copy number in cumulus cells and anti-Mullerian hormone level,female age, oocyte quality, embryo morphology, ploidy and blastocyst implantation rate? Summary answer A positive correlation of mtDNA quantity in CCs with the AMH,female age was revealed.There was no correlation between mtDNA quantity and embryo morphology,ploidy,implantation rate What is known already Recent studies have suggested that age-related decreased competence of oocytes may be due to low quantity of mtDNA copy number. Moreover, quantification of mtDNA in CCs may serve as an predictor of blastocysts viability. The purpose of this study is to investigate relative levels of mtDNA in the OCCCs in association with female age, ovarian reserve, embryo morphology, ploidy and blastocyst implantation rate. Study design, size, duration Prospective clinical study performed on 470 CCs retrieved from 72 advanced reproductive age patients undergoing ART treatment with intracytoplasmic sperm injection (ICSI) and preimplantation genetic testing for aneuploidy (PGT-A). Out of the 130 obtained blastocysts 56 embryos were diagnosed as aneuploid, and 74 as euploid. Presently, 51 frozen euploid embryos were transferred (FET). All transferred euploid blastocysts (n = 51) divided into 2 groups: 1 group (n = 21) - implanted embryos, 2 group (n = 30) - non-implanted. Participants/materials, setting, methods Inclusion criteria: age 35-45years;BMI: 18 – 24,9kg/m2; FSH ≤15IU/ml; normal female/male karyotype; non-smokers. Exclusion criteria: genital endometriosis III-IV;severe extragenital pathology; polycystic ovary syndrome; chronic endometritis; &amp;gt; 96% of sperm with abnormal morphology (WHO criteria). MtDNA was assessed by using a quantitative real-time polymerase chain reaction technique. DNA from the trophectoderm samples were amplified and subjected to aneuploidy analysis using array comparative genomic hybridization. In statistic analysis was used Pearson’s correlation coefficients and Fisher’s exact test; p &amp;lt; 0.05 was considered significant. Main results and the role of chance The median age was 37.8 years old (range, 35–45), the mean level of anti-Mullerian hormone (AMH) was 2.66±1.09, and the mean body mass index was 22.3±1.5. A positive correlation of the relative level of mtDNA in the CCs with the patients' age (p = 0.008) and AMH levels (p = 0.003) was revealed. There was no statistically significant correlation between mtDNA copy number and embryo morphology on day 5 (p = 0.7). There was a tendency to increase mtDNA copy number in group 1 vs. group 2, 390 and 299, respectively (p &amp;gt; 0.05). In this study we didn’t find relationship between median mtDNA content of CCs and embryos ploidy (356 vs. 325, in euploid (n = 74) and aneuploidy (n = 56) blastocyst, respectively, p &amp;gt; 0.05). Limitations, reasons for caution Our study was carried out in a relatively small subset of participants and obtained embryos. Correspondingly, the results obtained cannot be readily extrapolated on other groups of patients and need to be confirmed in larger trials. Wider implications of the findings This study showed that mtDNA quantification in CCs isn’t a useful biomarker for prediction embryos implantation potential or ploidy. MtDNA content in CCs correlated only with female age and AMH level. Trial registration number *

P-171 Identification of aneuploid embryos using cell free DNA in embryo culture medium

Abstract Study question Can noninvasive preimplantation genetic testing (PGT) using cell free DNA from embryo culture medium discriminate embryonic aneuploidy status? Summary answer Aneuploid embryos in older patients can be identified by cell free DNA in embryo culture medium. What is known already There have been reports of non-invasive PGT by analysing cell free DNA (cfDNA) released from embryos into culture medium, and found to be highly correlated with the analysis results of Trophectoderm (TE)-biopsy (Carmen.Rubio, 2020).We have initiated in 2021, a preliminary research program for the clinical application of niPGT. In aneuploid embryos, we have found a tendency for a high concordance rate between cfDNA analysis and blastocyst analysis results, suggesting the usefulness of cfDNA analysis in terms of identifying aneuploid embryos.Subsequently, we examined the usefulness of cfDNA analysis by comparing the concordance rate with cfDNA analysis and TE biopsy of blastocysts. Study design, size, duration After thawing pronuclear-stage frozen embryos for which consent was obtained for research use, they were co-cultured until Day 4, and then individually cultured on in new dishes.40 embryos that reached morula on day 4 or day 5 and blastocyst on day 6 or day 7 were included. Participants/materials, setting, methods The biopsied TE, the biopsied blastocyst, and the cfDNA obtained after individual culture were all sent to an external provider (Igenomix: Valencia, Spain) for chromosomal aneuploidy analysis by NGS. The concordance rate of the analysis for blastocysts in cfDNA and TE was calculated by dividing them into euploidy and aneuploidy, and by age. Concordance between the results of the blastocyst analysis and the culture medium were assessed according to the standards of the inspection company. Main results and the role of chance For the blastocyst analysis results, the concordance rate with cfDNA was 76.5% (26/34) and the concordance rate with TE was 85.3% (29/34), showing no difference. For the euploid blastocysts analyzed, the matching rate with cfDNA was 61.1% (11/18) and with TE was 77.8% (14/18), showing no difference. Similarly, for aneuploid blastocysts, the concordance rate with cfDNA was 93.8% (15/16) and with TE was 93.8% (15/16), showing no difference. Detailed analysis of aneuploid blastocysts revealed that the concordance rate with cfDNA was 88.9% (8/9) and the concordance rate with TE was 88.9% (8/9) in women under 39 years of age. In addition, the concordance rate with cfDNA was 100.0% (7/7) with TE was 100.0% (7/7) in those aged 40 and over. (Fisher's exact test) Limitations, reasons for caution Concordance between cfDNA and blastocyst analyzes in euploid embryos was low, continued follow-up is considered necessary. Wider implications of the findings In a detailed analysis of aneuploid blastocysts aged 40 years or older, Similar to TE, cfDNA showed a high concordance rate with the results of blastocyst analysis, demonstrating that cfDNA provides sufficient accuracy for identifying aneuploid embryos in women over 40 years of age. Trial registration number not applicable

O-107 Sperm chromosome chaos induced by MEIKIN gene mutations leads to blastocyst formation failure

Abstract Study question What are the effect and corresponding mechanisms of chromosome chaos of sperm caused by mutation of the MEIKIN gene on preimplantation embryo development? Summary answer Sperm chromosome chaos induced by MEIKIN gene mutations directly causes blastocyst formation failure by affecting the activation of the embryonic genome and lineage differentiation. What is known already In mice, Meikin is a meiosis-specific kinetochore factor that plays a crucial role in mono-orientation and protection of centromeric cohesion in meiosis I and the regulation of chromosome alignment during meiosis II. Both male and female Meikin gene knockout mice are completely infertile. Infertility in male Meikin-/- mice originates from defects in meiotic chromosome segregation and subsequent spermatogenesis. To our knowledge, no mutation of the MEIKIN gene has been reported in humans. Study design, size, duration In this study, semen from three patients with MEIKIN mutations and arrested embryos from one of them were analyzed to determine the effect of MEIKIN mutations on sperm and early embryonic development. Participants/materials, setting, methods Three male patients with MEIKIN mutations with a specific clinical phenotype were recruited. We assessed mutant sperm morphology using Papanicolaou staining. Sperm FISH and single sperm chromosome aneuploidy analysis（CNV-seq） were applied to identify mutant sperm Chromosomal abnormality. We also investigated the chromosome constitution and gene expression of the arrested embryos from one patient by parallel single-cell genome and transcriptome sequencing. Main results and the role of chance Novel mutations in the MEIKIN gene were identified in three infertility males with a specific clinical phenotype（They had good-quality embryos on day 3, but these embryos repeatedly failed to implant or develop to the blastocyst stage）. Routine semen assessments were conducted based on the WHO’s guidelines, and all these patients were diagnosed with oligoasthenoteratozoospermia. Sperm FISH showed that the frequencies of aneuploidies in spermatozoa were significantly higher than the normal control（89.05%,70.9%,93.24% vs. 5.03%）, and the CNV-seq analysis of single spermatozoa confirmed mutant sperm had severe chromosome chaos. Each cell of the arrested embryos from one patient had complicated chromosomal abnormalities, and the abnormal chromosomes were mainly derived from sperm. At the gene expression level, these embryos were arrested at the 8-cell to morula stage transition, and defects activation of a large ZGA and lineage specification genes led to blastocyst formation failure. Limitations, reasons for caution In this study, we discovered that mutations in MEIKIN caused male infertility manifesting as sperm chromosome chaos and blastocyst formation failure. However, the molecular mechanism of the sperm chromosome chaos involved in blastocyst formation needs to be further illuminated by using Meikin knockout mouse models. Wider implications of the findings We first reported that male with MEIKIN mutations is related to severe sperm chromosome abnormalities and blastocyst formation failure. Therefore, In the process of ICSI, if there are good-quality cleavage embryos that repeatedly fail to implant or develop to the blastocyst stage, it is recommended to examine male factors concurrently Trial registration number not applicable

Impact of male age on paternal aneuploidy: single-nucleotide polymorphism microarray outcomes following blastocyst biopsy

Does advanced paternal age (APA; ≥40 years) contribute to a higher incidence of paternal origin aneuploidy in preimplantation embryos? This was a multicentre retrospective study of single-nucleotide polymorphism (SNP) microarray (Natera and Karyomapping) preimplantation genetic testing (PGT) outcomes of blastocyst-stage embryos. Whole-chromosome aneuploidy analysis was performed on 2409 embryos from 389 male patients undertaking 681 assisted reproductive technology (ART) cycles between 2012-2021. Segmental aneuploidy analysis was performed on 867 embryos from 140 men undertaking 242 ART cycles between 2016-2021. Embryos were grouped based on paternal age at sperm collection: <35, 35-39 and ≥40 years. Paternal and maternal origin aneuploidy rates were compared between groups using chi-squared and/or Fisher's exact tests. There was no significant difference across groups in paternal origin whole-chromosome aneuploidy rate, overall (P=0.7561) or when segregated by type (trisomy and monosomy: P=0.2235 and 0.8156) or complexity (single versus 2, 3 or ≥4 aneuploidies: P=0.9733, 0.7517, 0.669 and 0.1481). Conversely, maternal origin whole-chromosome aneuploidy rate differed across groups (P<0.0001) in alignment with differing mean maternal age (P<0.001). Paternal origin deletions were 2.9-fold higher than maternal origin deletions (P=0.0084), independent of age stratification. No significant difference in paternal origin deletions was observed with APA ≥40 compared with the younger age groups (4.8% versus 2.5% and 2.8%, P=0.5292). Individual chromosome aneuploidy rates were too low to perform statistical comparisons. No significant association was found between APA and the incidence of paternal origin aneuploidy in preimplantation embryos, irrespective of type or complexity. Thus, APA may not be an indication for PGT.

A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data

Single-cell RNA sequencing is the reference technology to characterize the composition of the tumor microenvironment and to study tumor heterogeneity at high resolution. Here we report Single CEll Variational ANeuploidy analysis (SCEVAN), a fast variational algorithm for the deconvolution of the clonal substructure of tumors from single-cell RNA-seq data. It uses a multichannel segmentation algorithm exploiting the assumption that all the cells in a given copy number clone share the same breakpoints. Thus, the smoothed expression profile of every individual cell constitutes part of the evidence of the copy number profile in each subclone. SCEVAN can automatically and accurately discriminate between malignant and non-malignant cells, resulting in a practical framework to analyze tumors and their microenvironment. We apply SCEVAN to datasets encompassing 106 samples and 93,322 cells from different tumor types and technologies. We demonstrate its application to characterize the intratumor heterogeneity and geographic evolution of malignant brain tumors.

Live birth rate following frozen-thawed blastocyst transfer is higher in high-grade day 6 blastocysts than in low-grade day 5 blastocysts.

Day 5 (D5) blastocysts are generally given priority to transfer than day 6 (D6) blastocysts; however, which one should be prioritized to transfer when only low-grade D5 and high-grade D6 blastocysts are available? A large retrospective cohort study was carried out to evaluate the live birth rate (LBR) following D5 and D6 blastocysts in single frozen-thawed blastocyst transfer (FBT) during January 2014 and December 2018.A multivariate logistic regression was conducted to evaluate the combined impact of expansion day (D5 and D6) and blastocyst quality (high grade/low grade) on LBR, accounting for the potential confounding factors. The biopsied blastocysts from a consecutive PGT-A case series during February 2013 to December 2021 were analyzed in a supplementary study. The LBR achieved in high-grade D6 blastocyst transfer was significantly higher than that in low-grade D5 blastocyst transfer (50.43% vs. 40.70%, aOR 1.54, 95% CI 1.05-2.26, p = 0.027). There were no significant differences in preterm birth rate, very preterm birth rate, mean live birth weight, and birth weight <1,500 g and >4,000 g between the two cohorts. As for aneuploidy analysis in PGT, there were 54.55% of euploid blastocysts (30/55) among high-grade D6 blastocysts, significantly higher than the 41.39% of euploid blastocysts (565/1,365) among low-grade D5 blastocysts (p < 0.001). Our data suggest that D6 blastocysts with high morphology grading are preferred than D5 blastocysts with low morphology grading when selecting blastocyst transfer to shorten the time of conception.

Cytogenetic techniques in current biomedical research. PART III: numerical alterations of human karyotype

Numerical abnormalities of karyotype are the result of genome mutations. Unlike gene and chromosomal abnormalities, genome mutations do not disrupt the structure of DNA or chromosomes. The cause of numerical changes in the karyotype is a violation of the mechanism of chromosome segregation during meiosis or mitosis. Like other mutations, genome mutations are a natural mechanism for increasing of genetic diversity in offspring. At the same time, humans usually have negative effects of any numerical deviations from the norm, for this reason, cytogenetic examination of aneuploidies is an important diagnostic tool in medical genetics.A change in the number of sex chromosomes is usually not lethal. The spectrum of detected deviations in the carrier is from inconstant impairment of reproduction but a normal phenotype to malformations of some internal organs, infertility and severe intellectual disabilities. Aneuploidies of autosomes are always a threat to life and health. Only autosomal trisomies on chromosomes 13, 18, 21 and 22 are compatible with live birth, there are solitary reports of the birth of children with polyploidies. At the same time, the prognosis of life is relatively favorable only in the case of trisomy 21, leading to the formation of Down syndrome. Other aneuploidies usually lead to spontaneous termination of pregnancy in the early stages and are discovered in samples of abortion material.In this regard, cytogenetic analysis of chromosomal aneuploidies is used to establish the genetic cause of anomalies and malformations in the postnatal period, delays in speech and psychomotor development, reproduction disorders in adults. Of particular importance is the cytogenetic analysis of the karyotype of embryos in the prenatal period. The proposed lecture analyzes the mechanism of formation of genomic mutations and their diversity. The possible medical consequences of the presence of various types of aneuploidies are considered. To the reader attention is offered syndromes associated with a change in the number of chromosomes in the karyotype. The description is illustrated by real images of patient karyotypes.The lecture is aimed primarily at students of medical and biological specialties, young specialists who plan to use cytogenetic research methods in their practical activities, and doctors who are faced with the need to analyze and interpret the results of cytogenetic analysis. To assimilate the material under discussion, it is recommended to familiarize yourself with the previous lecture of the cycle.

Proteogenomic analysis of cancer aneuploidy and normal tissues reveals divergent modes of gene regulation across cellular pathways.

How cells control gene expression is a fundamental question. The relative contribution of protein-level and RNA-level regulation to this process remains unclear. Here, we perform a proteogenomic analysis of tumors and untransformed cells containing somatic copy number alterations (SCNAs). By revealing how cells regulate RNA and protein abundances of genes with SCNAs, we provide insights into the rules of gene regulation. Protein complex genes have a strong protein-level regulation while non-complex genes have a strong RNA-level regulation. Notable exceptions are plasma membrane protein complex genes, which show a weak protein-level regulation and a stronger RNA-level regulation. Strikingly, we find a strong negative association between the degree of RNA-level and protein-level regulation across genes and cellular pathways. Moreover, genes participating in the same pathway show a similar degree of RNA- and protein-level regulation. Pathways including translation, splicing, RNA processing, and mitochondrial function show a stronger protein-level regulation while cell adhesion and migration pathways show a stronger RNA-level regulation. These results suggest that the evolution of gene regulation is shaped by functional constraints and that many cellular pathways tend to evolve one predominant mechanism of gene regulation at the protein level or at the RNA level.

Non-invasive prenatal testing for the detection of trisomy 13, 18, and 21 and sex chromosome aneuploidies in 68,763 cases.

Objectives: Non-invasive prenatal testing (NIPT) has been widely used in recent years. According to clinical experience from all hospitals providing prenatal screening services in Beijing, we explored the feasibility of using NIPT for the analysis of common foetal aneuploidies among pregnancies. Methods: In total, 68,763 maternal blood samples were collected from January 2020 to December 2020 at the Beijing prenatal diagnosis agency. Cases with positive screening results by NIPT detection were validated using prenatal diagnosis. Results: In total, 920 cases had a high-risk NIPT result, and 755 cases were shown to be truly positive by a chromosome karyotyping analysis; the prenatal diagnosis rate was 82.07% (755/920). Of the920 cases, there were 164 cases of T21, 70 cases of T18, 38 cases of T13, 360 cases of SCAs and 288 cases of other chromosomal abnormalities. The positive rates of T21, T18, T13, and SCAs were 0.24% (164/68,763), 0.10% (70/68,763), 0.06% (38/68,763) and 0.52% (360/68,763), respectively. The sensitivity and specificity were 98.17% and 99.92% for T21, 96.15% and 99.93% for T18, and 100% and 99.95% for T13, respectively. The PPVs of T21,T18,T13 and SCAs were65.24% (107/164), 35.71% (25/70), 18.42% (7/38) and 31.39% (113/360), respectively. For all indications, there were more higher T21/18/13 in the high-risk group than in the low-risk group (comprising only cases of voluntary request), with a positive rate of 0.46% vs. 0.27% (p < 0.001), sensitivity of 99.16% vs. 91.30% (p = 0.02) and PPV of 56.73%vs.32.81% (p = 0.001), but there was no significant difference in specificity between the groups (p = 0.71). The detection indication with the highest PPV (100%) by NIPT was ultrasound structural abnormalities and ultrasound soft marker abnormalities for T21 and ultrasound structural abnormalities and NT thickening for T18 and T13. The PPVs of different clinical indications of T21 (p = 0.002), T13 (p = 0.04) and SACs (p = 0.02) were statistically significant. Conclusion: The high specificity, efficiency and safety (non-invasiveness) of NIPT can effectively improve the detection rate of common chromosomal aneuploidy, thereby reducing the occurrence of birth defects. We should encourage pregnant women with NIPT-high-risk results to undergo a prenatal diagnosis to determine whether the foetus has chromosomal abnormalities. More importantly, the screening efficiency of NIPT in the low-risk group was significantly lower than that in the high-risk group. Therefore, the use of NIPT in low-risk groups should be fully promoted, and socioeconomic benefits should be considered.

DNA aneuploidy combined with radial EBUS in the diagnosis of peripheral lung lesions.

To explore the diagnostic value of DNA aneuploidy analysis combined with radial endobronchial ultrasound (R-EBUS)-guided transbronchial biopsy in peripheral lung lesions. We performed a retrospective analysis of patients who underwent R-EBUS examination. DNA aneuploidy analysis of bronchial washing from the target bronchial segment were performed. The clinical information, R-EBUS data, pathological results and DNA image cytometry (DNA-ICM) results were collected. For patients who did not have a clear diagnosis after bronchoscopy, follow-up data was recorded. A total of 42 cases were included. Thirty patients had confirmed malignant tumor of the lung, 19 of which were confirmed by pathology after bronchoscopy, and 11 cases were confirmed later by surgery or percutaneous lung puncture. Twelve patients were finally considered to have benign lesions. The sensitivity of R-EBUS is 63.3% and the specificity is 100%. DNA-ICM has a sensitivity of 76.7% and a specificity of 91.7%. When combined, they have a sensitivity of 90%, and specificity 91.7%. As for malignant lesions, we further analyzed smoking, the size and location of lesions on chest CT, the number of aneuploid cells and the maximum value of DNA content. The results indicated that increased number of aneuploid cells or increased max value of DNA content may predict higher probability of malignancy. DNA-ICM combined with R-EBUS can improve the diagnostic sensitivity of malignant peripheral lung lesions. Increased number of aneuploid cells or increased max value of DNA content may indicate that the lesions are more likely to be malignant.

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform.

Next-generation sequencing has gained increasing importance in the clinical application in the determination of genetic variants. In the pre-implantation genetic test, this technique has its unique advantages in scalability, throughput, and cost. For the pre-implantation genetic test for aneuploidy analysis, the semiconductor-based next-generation sequencing (NGS) system presented here provides a comprehensive approach to determine structural genetic variants at a minimum resolution of 8 Mb. From sample acquisition to the final report, the working process requires multiple steps with close adherence to protocols. Since various critical steps could determine the outcome of amplification, quality of the library, coverage of reads, and output of data, descriptive information with visual demonstration other than words could offer more detail to the operation and manipulation, which may have a great impact on the results of all critical steps. The methods presented herein will display the procedures involved in whole genome amplification (WGA) of biopsied Trophectoderm (TE) cells, genomic library construction, sequencer management, and finally, generating copy number variants' reports.