Genome-Wide Copy Number Alteration Detection in Preimplantation Genetic Diagnosis

2017 ◽  
pp. 27-42 ◽  
Author(s):  
Lieselot Deleye ◽  
Dieter De Coninck ◽  
Dieter Deforce ◽  
Filip Van Nieuwerburgh
Keyword(s):  
Preimplantation Genetic Diagnosis ◽  
Copy Number ◽  
Copy Number Alteration ◽  
Genetic Diagnosis ◽  
Genome Wide

Transfer of aneuploid embryos following preimplantation genetic diagnosis: the added value of a haplotyping-based genome-wide approach

2018 ◽  
Vol 36 ◽  
pp. e23
Author(s):  
Cindy Melotte ◽  
Eftychia Dimitriadou ◽  
Sophie Debrock ◽  
Koen Devriendt ◽  
Thomy De Ravel ◽  
...  
Keyword(s):  
Preimplantation Genetic Diagnosis ◽  
Genetic Diagnosis ◽  
Added Value ◽  
Genome Wide

scholarly journals Genome-wide Hypomethylation in Human Glioblastomas Associated with Specific Copy Number Alteration, Methylenetetrahydrofolate Reductase Allele Status, and Increased Proliferation

2006 ◽  
Vol 66 (17) ◽  
pp. 8469-8476 ◽  
Author(s):  
Benoît Cadieux ◽  
Tsui-Ting Ching ◽  
Scott R. VandenBerg ◽  
Joseph F. Costello
Keyword(s):  
Copy Number ◽  
Copy Number Alteration ◽  
Methylenetetrahydrofolate Reductase ◽  
Genome Wide ◽  
Allele Status

Abstract 3410: Hodgkin and Reed-Sternberg cells genome-wide copy number alteration analysis at single cell level by high-throughput automated platforms

2019 ◽  
Author(s):  
Andrea Raspadori ◽  
Paola Tononi ◽  
Chiara Mangano ◽  
Marianna Garonzi ◽  
Claudio Forcato ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Copy Number ◽  
Copy Number Alteration ◽  
Single Cell Level ◽  
Cell Level ◽  
Genome Wide

Abstract 3410: Hodgkin and Reed-Sternberg cells genome-wide copy number alteration analysis at single cell level by high-throughput automated platforms

2019 ◽  
Author(s):  
Andrea Raspadori ◽  
Paola Tononi ◽  
Chiara Mangano ◽  
Marianna Garonzi ◽  
Claudio Forcato ◽  
...  
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Copy Number ◽  
Copy Number Alteration ◽  
Single Cell Level ◽  
Cell Level ◽  
Genome Wide

Genome wide karyomapping for preimplantation genetic diagnosis (PGD) detects inherited chromosomal aneuploidies

2009 ◽  
Vol 92 (3) ◽  
pp. S204
Author(s):  
A.H. Handyside ◽  
N.H. Zech ◽  
B. Mariani ◽  
G.L. Harton
Keyword(s):  
Preimplantation Genetic Diagnosis ◽  
Genetic Diagnosis ◽  
Genome Wide ◽  
Chromosomal Aneuploidies

scholarly journals SNP array-based copy number and genotype analyses for preimplantation genetic diagnosis of human unbalanced translocations

2012 ◽  
Vol 20 (9) ◽  
pp. 938-944 ◽  
Author(s):  
Chris MJ van Uum ◽  
Servi JC Stevens ◽  
Joseph CFM Dreesen ◽  
Marion Drüsedau ◽  
Hubert J Smeets ◽  
...  
Keyword(s):  
Preimplantation Genetic Diagnosis ◽  
Copy Number ◽  
Snp Array ◽  
Genetic Diagnosis

Genome-wide somatic copy number alteration analysis and database construction for cervical cancer

2020 ◽  
Vol 295 (3) ◽  
pp. 765-773 ◽  
Author(s):  
Hong Luo ◽  
Xiaohan Xu ◽  
Jian Yang ◽  
Kun Wang ◽  
Chen Wang ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Copy Number ◽  
Copy Number Alteration ◽  
Database Construction ◽  
Genome Wide ◽  
Somatic Copy Number Alteration

scholarly journals Machine learning modeling of genome-wide copy number alteration signatures reliably predicts IDH mutational status in adult diffuse glioma

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Nicholas Nuechterlein ◽  
Linda G. Shapiro ◽  
Eric C. Holland ◽  
Patrick J. Cimino
Keyword(s):  
Machine Learning ◽  
Copy Number ◽  
Copy Number Alteration ◽  
Molecular Subtype ◽  
The Cancer Genome Atlas ◽  
Diffuse Glioma ◽  
Mutational Status ◽  
Genome Wide ◽  
Diffuse Gliomas ◽  
Rigorous Model

AbstractKnowledge of 1p/19q-codeletion and IDH1/2 mutational status is necessary to interpret any investigational study of diffuse gliomas in the modern era. While DNA sequencing is the gold standard for determining IDH mutational status, genome-wide methylation arrays and gene expression profiling have been used for surrogate mutational determination. Previous studies by our group suggest that 1p/19q-codeletion and IDH mutational status can be predicted by genome-wide somatic copy number alteration (SCNA) data alone, however a rigorous model to accomplish this task has yet to be established. In this study, we used SCNA data from 786 adult diffuse gliomas in The Cancer Genome Atlas (TCGA) to develop a two-stage classification system that identifies 1p/19q-codeleted oligodendrogliomas and predicts the IDH mutational status of astrocytic tumors using a machine-learning model. Cross-validated results on TCGA SCNA data showed near perfect classification results. Furthermore, our astrocytic IDH mutation model validated well on four additional datasets (AUC = 0.97, AUC = 0.99, AUC = 0.95, AUC = 0.96) as did our 1p/19q-codeleted oligodendroglioma screen on the two datasets that contained oligodendrogliomas (MCC = 0.97, MCC = 0.97). We then retrained our system using data from these validation sets and applied our system to a cohort of REMBRANDT study subjects for whom SCNA data, but not IDH mutational status, is available. Overall, using genome-wide SCNAs, we successfully developed a system to robustly predict 1p/19q-codeletion and IDH mutational status in diffuse gliomas. This system can assign molecular subtype labels to tumor samples of retrospective diffuse glioma cohorts that lack 1p/19q-codeletion and IDH mutational status, such as the REMBRANDT study, recasting these datasets as validation cohorts for diffuse glioma research.

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