scholarly journals Next Generation Sequencing Detects Premeiotic Errors in Human Oocytes

2022 ◽  
Vol 23 (2) ◽  
pp. 665
Author(s):  
Harita Ghevaria ◽  
Sioban SenGupta ◽  
Roy Naja ◽  
Rabi Odia ◽  
Holly Exeter ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Polar Body ◽  
Independent Study ◽  
Comparative Genomic ◽  
Next Generation ◽  
Consistent Finding ◽  
Autosomal Aneuploidy ◽  
First Polar Body ◽  
Germinal Mosaicism ◽  
Generation Sequencing

Autosomal aneuploidy is the leading cause of embryonic and foetal death in humans. This arises mainly from errors in meiosis I or II of oogenesis. A largely ignored source of error stems from germinal mosaicism, which leads to premeiotic aneuploidy. Molecular cytogenetic studies employing metaphase fluorescence in situ hybridization and comparative genomic hybridisation suggest that premeiotic aneuploidy may affect 10–20% of oocytes overall. Such studies have been criticised on technical grounds. We report here an independent study carried out on unmanipulated oocytes that have been analysed using next generation sequencing (NGS). This study confirms that the incidence of premeiotic aneuploidy in an unselected series of oocytes exceeds 10%. A total of 140 oocytes donated by 42 women gave conclusive results; of these, 124 (88.5%) were euploid. Sixteen out of 140 (11.4%) provided evidence of premeiotic aneuploidy. Of the 140, 112 oocytes were immature (germinal vesicle or metaphase I), of which 10 were aneuploid (8.93%); the remaining 28 were intact metaphase II - first polar body complexes, and six of these were aneuploid (21.4%). Of the 16 aneuploid cells, half contained simple errors (one or two abnormal chromosomes) and half contained complex errors. We conclude that germinal mosaicism leading to premeiotic aneuploidy is a consistent finding affecting at least 10% of unselected oocytes from women undergoing egg collection for a variety of reasons. The importance of premeiotic aneuploidy lies in the fact that, for individual oocytes, it greatly increases the risk of an aneuploid mature oocyte irrespective of maternal age. As such, this may account for some cases of aneuploid conceptions in very young women.

The novel approach to distinguish primary multiple lung adenocarcinomas from intrapulmonary metastases by next generation sequencing in Chinese patients.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e20506-e20506
Author(s):  
Lin Li ◽  
Naiquan Mao ◽  
Yingcheng Lyu ◽  
Huayue Lin ◽  
Kefeng Wang ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Next Generation Sequencing ◽  
Chinese Patients ◽  
Comparative Genomic ◽  
Genomic Profiling ◽  
Next Generation ◽  
Architectural Patterns ◽  
Chinese Cohort ◽  
Lung Adenocarcinomas ◽  
Generation Sequencing

e20506 Background: Differentiation of multiple primary lung cancer (MPLC) from intrapulmonary metastasis (IPM) is critical to determine clinical stage. Although clinicopathological features could provide certain evidences, it’s still challenging to identify the tumor malignancy accurately. In General, standard histopathologic approach is adequate in most cases, but has notable limitations in the recognition of IPMs. Herein, we propose an integrated molecular algorithm to facilitate MPLCs and IPMs diagnosis in the clinical practice. Methods: 40 Chinese patients with lung adenocarcinomas were enrolled in the study, 84 tumor samples were collected for next-generation sequencing. Somatic alterations with variant allele fraction (VAF) ≥1% were taken into account for molecular algorithm. A genomic database of 2,471 Chinese lung adenocarcinomas (LUAD) was used to calculate odds of coincidental occurrence, prevalence of individual mutation prevalence. Tumor relatedness diagnosed by histopathologic assessment was contrasted with comparative genomic profiling by subsequent NGS. Moreover, the performance of molecular algorithm prediction was evaluated as well. Results: Firstly, we compared the performance of comprehensive next-generation sequencing (NGS) with standard histopathologic approaches for distinguishing NSCLC subtypes in clinical practice. The genomic profiling was described as following: EGFR alterations occurred more frequently in MPLCs compared to IPMs (77.1% vs 50.0%, P<0.05). Further analysis showed that TP53 alterations occurred less frequently in MPLCs compared to large Chinese cohort (22.9% vs 51.0%, P<0.05). TP53 alterations occurred less frequently in MPLCs compared to large Chinese cohort (P<0.05). The classifications based on the three different methodologies mentioned above were compared. Molecular algorithm prediction was concordant with NGS in 21 cases (52.5%), particularly in the prediction of MPLC. Retrospective review highlighted several histologic challenges, including morphologic progression in some IPMs. For the five undetermined cases, two showed differences in architectural patterns, and remained cases have nodules presented as adenocarcinoma in situ, or minimally invasive adenocarcinoma. Of 28 MPLC cases defined by NGS, 25 cases had unique somatic mutations per pair Based on calculation from the prevalence of EGFR L858R mutation (27%) in large Chinese cohort, the odds of coincidental occurrence of the mutation in two unrelated tumors was 7.3%. Taking together, EGFR alterations occurred more frequently in MPLCs compared to IPMs (77.1% vs 50.0%, P<0.05). Molecular algorithm prediction was concordant with NGS in 21 cases (52.5%). Conclusions: Our results support broad panel NGS to assist differential diagnosis to assist approach in clinical practice. It is necessary to conduct large clinical study to establish comprehensive algorithm models to assist diagnosis and predict clinical outcome.

scholarly journals P14.127 From next generation sequencing and comparative genomic hybridization to personalised medicine for adult primary brain tumors: the profiler trial

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii99-iii99
Author(s):  
A Bonneville-levard ◽  
D Frappaz ◽  
D Pissaloux ◽  
Q Wang ◽  
D Perol ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Targeted Therapy ◽  
Next Generation Sequencing ◽  
Brain Tumors ◽  
Comparative Genomic Hybridization ◽  
Comparative Genomic ◽  
Next Generation ◽  
Genomic Hybridization ◽  
Primary Brain Tumors ◽  
Generation Sequencing

Abstract BACKGROUND Personalized anti-tumoral therapies may currently be proposed on the basis of immuno-histochemistry, but also next-generation sequencing and comparative genomic hybridization. ProfiLER trial explored the feasibility, efficacy and the impact of molecular profiling for patients with solid or hematological advanced cancers including brain tumors. MATERIAL AND METHODS Patients with primary brain tumors, pre-treated with at least one line of anti-cancer treatment, could be included in this multicentric prospective trial. A molecular profile (next-generation sequencing and comparative genomic hydridization) was established on fresh or archived sample. Weekly molecular tumor board analysed results to propose as far as possible a molecular targeted therapy. RESULTS between February 2013 and December 2015, 141 patients with primary brain tumor were enrolled. One hundred five samples were further analyzed as 30 samples were excluded, and 6 are on-going. The rate of screen failure was 16/33 for stereotactic biopsy (49%) versus 11/104 (11%) for removal. The main representative histologic type of tumors were glioblastoma (n=46, 43,8%), low grade glioma (n=26, 24,8%), high grade glioma (n=12, 11,4%) and atypical and anaplastic meningioma (n=8, 7,6%). Median delay between the diagnostic of the primitive tumor and the inclusion in ProfiLER study was 2.7 years (0.2 - 29 years). Median delay between the consent and the results of the multidisciplinary meeting was 2.8 months (1–7.1 months). Forty-three patients (41%) presented at least one “druggable molecular alteration”. The most frequently altered genes were CDKN2A (n=18, 29%), EGFR (n=12, 20%), PDGFRa (n=8, 13%), PTEN (n=8, 13%), CDK4 (n=7, 11%), KIT (n=6, 10%), PIK3CA (n=5, 8%), MDM2 (n=3, 5%). Sixteen patients could not have a proposition of specific treatment due to death before MBT (n=5, 31.3%), lack of available clinical trials (n=9, 56%), or ambiguous results (n=2, 12.5%). Among the 27 patients (26%) for whom a specific therapy has been proposed, only six patients ultimately received a medical targeted therapy (everolimus n=3, erlotinib n=1, ruloxitinib n=1, sorafenib n=1). Four patients discontinued the treatment for toxicity, the 2 others for clinical progression. CONCLUSION routine high-throughput sequencing is feasible for brain tumors but delays should be reduced to be able to propose targeted therapies to patients fit enough to benefit from experimental treatment. Macroscopic surgery is the best way to obtain workable samples. Specific panel genes for neurologic tumors should be developed, as well as change of practices concerning exclusion criteria in clinical trials.

scholarly journals Validation of Next-Generation Sequencing and Array Comparative Genomic Hybridization for Diagnosis and Screening of Reciprocal and Robertsonian Translocations in Human Blastocysts

2020 ◽  
Author(s):  
Shengrong Du ◽  
Yun-Hong Lin ◽  
Yan Sun ◽  
Qing-Fen Chen ◽  
Zhi-Qing Huang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Cell Mass ◽  
Comparative Genomic ◽  
Next Generation ◽  
Genomic Hybridization ◽  
Robertsonian Translocations ◽  
Significant Difference ◽  
Generation Sequencing

Abstract Background: Advances in biotechnology, especially next-generation sequencing (NGS) and array comparative genomic hybridization (aCGH) approaches, have improved preimplantation genetic screening; however, these methods have not been directly compared. This study was carried out to identify the more promising method for screening reciprocal and Robertsonian translocations. Here, blastocysts from carriers with reciprocal and Robertsonian translocations were retrospectively evaluated and results from preimplantation genetic testing in 272 blastocytes were analysed for parental unbalanced translocations using aCGH and NGS. Results: There was no significant difference in the no embryo-transfer rate between aCGH and NGS. Among 59 blastocysts screened in the aCGH group, 32.76% were normal embryos and 67.24% were abnormal embryos, including 36.21% embryos with a translocation, 17.24% with no translocation, and 15.52% with combined abnormalities. Similar results were obtained from the 214 blastocysts tested in the NGS group. In women <35-years, more normal blastocysts were identified in the NGS group compared to the aCGH group. There was a higher rate of euploidy among blastocysts with higher quality grades in the NGS group than in the aCGH group for the trophectoderm (43.51% vs 29.41%) and inner cell mass (59.11% vs 25.00%). Conclusion: Equivalent clinical findings were observed for aCGH and NGS for parental reciprocal chromosomal translocations. However, NGS has the potential to overcome the inherent limitations of aCGH, including the detection of mosaicism and smaller partial gains/losses, thereby providing improvements in the detection of euploid blastocysts, along with enhanced reliability and sensitivity.

scholarly journals Development and Validation of a 34-Gene Inherited Cancer Predisposition Panel Using Next-Generation Sequencing

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Sun Hee Rosenthal ◽  
Weimin Sun ◽  
Ke Zhang ◽  
Yan Liu ◽  
Quoclinh Nguyen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cancer Risk ◽  
Validation Study ◽  
Cancer Predisposition ◽  
Comparative Genomic ◽  
Next Generation ◽  
Significant Information ◽  
Inherited Cancer ◽  
Cancer Syndromes ◽  
Generation Sequencing

The use of genetic testing to identify individuals with hereditary cancer syndromes has been widely adopted by clinicians for management of inherited cancer risk. The objective of this study was to develop and validate a 34-gene inherited cancer predisposition panel using targeted capture-based next-generation sequencing (NGS). The panel incorporates genes underlying well-characterized cancer syndromes, such as BRCA1 and BRCA2 (BRCA1/2), along with more recently discovered genes associated with increased cancer risk. We performed a validation study on 133 unique specimens, including 33 with known variant status; known variants included single nucleotide variants (SNVs) and small insertions and deletions (Indels), as well as copy-number variants (CNVs). The analytical validation study achieved 100% sensitivity and specificity for SNVs and small Indels, with 100% sensitivity and 98.0% specificity for CNVs using in-house developed CNV flagging algorithm. We employed a microarray comparative genomic hybridization (aCGH) method for all specimens that the algorithm flags as CNV-positive for confirmation. In combination with aCGH confirmation, CNV detection specificity improved to 100%. We additionally report results of the first 500 consecutive specimens submitted for clinical testing with the 34-gene panel, identifying 53 deleterious variants in 13 genes in 49 individuals. Half of the detected pathogenic/likely pathogenic variants were found in BRCA1 (23%), BRCA2 (23%), or the Lynch syndrome-associated genes PMS2 (4%) and MLH1 (2%). The other half were detected in 9 other genes: MUTYH (17%), CHEK2 (15%), ATM (4%), PALB2 (4%), BARD1 (2%), CDH1 (2%), CDKN2A (2%), RAD51C (2%), and RET (2%). Our validation studies and initial clinical data demonstrate that a 34-gene inherited cancer predisposition panel can provide clinically significant information for cancer risk assessment.

scholarly journals Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Tiancheng Liu ◽  
Lin Yu ◽  
Lei Liu ◽  
Hong Li ◽  
Yixue Li
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
New Technology ◽  
Evolutionary Model ◽  
Evolutionary Developmental Biology ◽  
Comparative Genomic ◽  
Next Generation ◽  
Next Generation Sequencing Technology ◽  
Evo Devo ◽  
Generation Sequencing

High throughput technology has prompted the progressive omics studies, including genomics and transcriptomics. We have reviewed the improvement of comparative omic studies, which are attributed to the high throughput measurement of next generation sequencing technology. Comparative genomics have been successfully applied to evolution analysis while comparative transcriptomics are adopted in comparison of expression profile from two subjects by differential expression or differential coexpression, which enables their application in evolutionary developmental biology (EVO-DEVO) studies. EVO-DEVO studies focus on the evolutionary pressure affecting the morphogenesis of development and previous works have been conducted to illustrate the most conserved stages during embryonic development. Old measurements of these studies are based on the morphological similarity from macro view and new technology enables the micro detection of similarity in molecular mechanism. Evolutionary model of embryo development, which includes the “funnel-like” model and the “hourglass” model, has been evaluated by combination of these new comparative transcriptomic methods with prior comparative genomic information. Although the technology has promoted the EVO-DEVO studies into a new era, technological and material limitation still exist and further investigations require more subtle study design and procedure.

scholarly journals Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pierre-Julien Viailly ◽  
Vincent Sater ◽  
Mathieu Viennot ◽  
Elodie Bohers ◽  
Nicolas Vergne ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
B Cell Lymphoma ◽  
Copy Number Variations ◽  
Comparative Genomic ◽  
Detection Accuracy ◽  
Next Generation ◽  
Tumor Suppressor Gene Inactivation ◽  
Generation Sequencing ◽  
Cnv Detection

Abstract Background Recently, copy number variations (CNV) impacting genes involved in oncogenic pathways have attracted an increasing attention to manage disease susceptibility. CNV is one of the most important somatic aberrations in the genome of tumor cells. Oncogene activation and tumor suppressor gene inactivation are often attributed to copy number gain/amplification or deletion, respectively, in many cancer types and stages. Recent advances in next generation sequencing protocols allow for the addition of unique molecular identifiers (UMI) to each read. Each targeted DNA fragment is labeled with a unique random nucleotide sequence added to sequencing primers. UMI are especially useful for CNV detection by making each DNA molecule in a population of reads distinct. Results Here, we present molecular Copy Number Alteration (mCNA), a new methodology allowing the detection of copy number changes using UMI. The algorithm is composed of four main steps: the construction of UMI count matrices, the use of control samples to construct a pseudo-reference, the computation of log-ratios, the segmentation and finally the statistical inference of abnormal segmented breaks. We demonstrate the success of mCNA on a dataset of patients suffering from Diffuse Large B-cell Lymphoma and we highlight that mCNA results have a strong correlation with comparative genomic hybridization. Conclusion We provide mCNA, a new approach for CNV detection, freely available at https://gitlab.com/pierrejulien.viailly/mcna/ under MIT license. mCNA can significantly improve detection accuracy of CNV changes by using UMI.

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