scholarly journals Critical evaluation of copy number variant calling methods using DNA methylation

2019 ◽  
Vol 44 (2) ◽  
pp. 148-158
Author(s):  
Varun Kilaru ◽  
Anna K. Knight ◽  
Seyma Katrinli ◽  
Dawayland Cobb ◽  
Adriana Lori ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Copy Number ◽  
Critical Evaluation ◽  
Variant Calling ◽  
Copy Number Variant

scholarly journals tHapMix: simulating tumour samples through haplotype mixtures

2016 ◽  
Author(s):  
Sergii Ivakhno ◽  
Camilla Colombo ◽  
Stephen Tanner ◽  
Philip Tedder ◽  
Stefano Berri ◽  
...  
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Variant Calling ◽  
Copy Number Variant ◽  
Supplementary Information ◽  
Genome Diversity ◽  
Simulation Framework ◽  
Somatic Genome ◽  
Copy Number Changes ◽  
Sequencing Platforms

AbstractMotivationLarge-scale rearrangements and copy number changes combined with different modes of cloevolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable oriant calling tools and create well-calibrated benchmarks.ResultsWe developed a new simulation framework tHapMix that enables the creation of tumour samples with different ploidy, purity and polyclonality features. It easily scales to simulation of hundreds of somatic genomes, while re-use of real read data preserves noise and biases present in sequencing platforms. We further demonstrate tHapMix utility by creating a simulated set of 140 somatic genomes and showing how it can be used in training and testing of somatic copy number variant calling tools.Availability and implementationtHapMix is distributed under an open source license and can be downloaded from https://github.com/Illumina/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals Copy number variant calling on a 177 gene expanded carrier screening panel reveals impact of hbb deletions

2017 ◽  
Vol 108 (3) ◽  
pp. e282
Author(s):  
K.A. Beauchamp ◽  
P. Grauman ◽  
G.J. Hogan ◽  
K.R. Haas ◽  
G.M. Gould ◽  
...  
Keyword(s):  
Copy Number ◽  
Variant Calling ◽  
Copy Number Variant ◽  
Carrier Screening ◽  
Expanded Carrier Screening

scholarly journals DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Michael D. Linderman ◽  
Davin Chia ◽  
Forrest Wallace ◽  
Frank A. Nothaft
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Variant Calling ◽  
Copy Number Variant ◽  
Read Depth ◽  
Lessons Learned ◽  
Apache Spark ◽  
Sequencing Data ◽  
Whole Exome Sequencing Data ◽  
Genome Analyses

Abstract Background XHMM is a widely used tool for copy-number variant (CNV) discovery from whole exome sequencing data but can require hours to days to run for large cohorts. A more scalable implementation would reduce the need for specialized computational resources and enable increased exploration of the configuration parameter space to obtain the best possible results. Results DECA is a horizontally scalable implementation of the XHMM algorithm using the ADAM framework and Apache Spark that incorporates novel algorithmic optimizations to eliminate unneeded computation. DECA parallelizes XHMM on both multi-core shared memory computers and large shared-nothing Spark clusters. We performed CNV discovery from the read-depth matrix in 2535 exomes in 9.3 min on a 16-core workstation (35.3× speedup vs. XHMM), 12.7 min using 10 executor cores on a Spark cluster (18.8× speedup vs. XHMM), and 9.8 min using 32 executor cores on Amazon AWS’ Elastic MapReduce. We performed CNV discovery from the original BAM files in 292 min using 640 executor cores on a Spark cluster. Conclusions We describe DECA’s performance, our algorithmic and implementation enhancements to XHMM to obtain that performance, and our lessons learned porting a complex genome analysis application to ADAM and Spark. ADAM and Apache Spark are a performant and productive platform for implementing large-scale genome analyses, but efficiently utilizing large clusters can require algorithmic optimizations and careful attention to Spark’s configuration parameters.

Review of 12 months of copy number variant calling on a clinical next generation sequencing pipeline

Pathology ◽  
2020 ◽  
Vol 52 ◽  
pp. S108
Author(s):  
Dylan A. Mordaunt ◽  
Julien Soubrier ◽  
Song Gao ◽  
Lesley Rawlings ◽  
Jillian Nicholl ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Variant Calling ◽  
Copy Number Variant ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals 259: Copy number variant calling on a 176-disease expanded carrier screening panel

2018 ◽  
Vol 218 (1) ◽  
pp. S166
Author(s):  
Dale Muzzey ◽  
Kyle A. Beauchamp ◽  
Peter Grauman ◽  
Gregory J. Hogan ◽  
Kevin R. Haas ◽  
...  
Keyword(s):  
Copy Number ◽  
Variant Calling ◽  
Copy Number Variant ◽  
Carrier Screening ◽  
Expanded Carrier Screening

scholarly journals A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

2012 ◽  
Vol 28 (21) ◽  
pp. 2747-2754 ◽  
Author(s):  
Vincent Plagnol ◽  
James Curtis ◽  
Michael Epstein ◽  
Kin Y. Mok ◽  
Emma Stebbings ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Count Data ◽  
Copy Number ◽  
Variant Calling ◽  
Copy Number Variant ◽  
Read Count ◽  
Robust Model

scholarly journals Copy number-dependent DNA methylation of the Pyricularia oryzae MAGGY retrotransposon is triggered by DNA damage

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Ba Van Vu ◽  
Quyet Nguyen ◽  
Yuki Kondo-Takeoka ◽  
Toshiki Murata ◽  
Naoki Kadotani ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Copy Number ◽  
Rna Silencing ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Pyricularia Oryzae ◽  
Transcriptional Gene Silencing ◽  
Physical Interaction ◽  
Uncharacterized Protein ◽  
Form Complex

AbstractTransposable elements are common targets for transcriptional and post-transcriptional gene silencing in eukaryotic genomes. However, the molecular mechanisms responsible for sensing such repeated sequences in the genome remain largely unknown. Here, we show that machinery of homologous recombination (HR) and RNA silencing play cooperative roles in copy number-dependent de novo DNA methylation of the retrotransposon MAGGY in the fungusPyricularia oryzae. Genetic and physical interaction studies revealed thatRecAdomain-containing proteins, includingP. oryzaehomologs ofRad51, Rad55, andRad57, together with an uncharacterized protein, Ddnm1, form complex(es) and mediate either the overall level or the copy number-dependence of de novo MAGGY DNA methylation, likely in conjunction with DNA repair. Interestingly,P. oryzaemutants of specific RNA silencing components (MoDCL1andMoAGO2)were impaired in copy number-dependence of MAGGY methylation. Co-immunoprecipitation of MoAGO2 and HR components suggested a physical interaction between the HR and RNA silencing machinery in the process.

scholarly journals EPCO-29. EPIGENOMICS OF THE GLIOMA LONGITUDINAL ANALYSIS (GLASS) CONSORTIUM

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii75-ii75
Author(s):  
Thais Sabedot ◽  
Michael Wells ◽  
Indrani Datta ◽  
Tathiane Malta ◽  
Ana Valeria Castro ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Longitudinal Analysis ◽  
Copy Number ◽  
Large Scale ◽  
Molecular Classification ◽  
Tumor Burden ◽  
Copy Number Alterations ◽  
Unsupervised Analysis ◽  
Diffuse Gliomas ◽  
New Biomarkers

Abstract Adult diffuse gliomas are central nervous system (CNS) tumors that arise from the malignant transformation of glial cells. Nearly all gliomas will recur despite standard treatment however, current histopathological grading fails to predict which of them will relapse and/or progress. The Glioma Longitudinal AnalySiS (GLASS) consortium is a large-scale collaboration that aims to investigate the molecular profiling of matched primary and recurrent glioma samples from multiple institutions in order to better understand the dynamic evolution of these tumors. At this time, the cohort comprises 946 samples across 11 institutions and among those, 864 have DNA methylation data available. The current molecular classification based on 7 subtypes published by TCGA in 2016 was applied to the dataset. Among the IDH wildtype tumors, 33% (16/49) of the patients showed a change of subtype upon recurrence, whereas most of them (9/16) were Classic-like at the primary stage but changed to either Mesenchymal-like or PA-like at the recurrent level. Among the IDH mutant tumors, 15% (22/142) showed a change of subtype at recurrent stage, in which 16 out of 22 progressed from G-CIMP-high to G-CIMP-low. Although some tumors progressed to a different subtype upon recurrence, an unsupervised analysis showed that the samples tend to cluster by patient instead of by subtype. By estimating the copy number alterations of these tumors using DNA methylation, the overall copy number profile of the recurrent samples remains similar to their primary counterpart. From this initial analysis using epigenomic data, we were able to characterize some aspects of glioma evolution and how the DNA methylation is associated with the progression of these tumors to different subtypes. These findings corroborate the importance of epigenetics in gliomas and can potentially lead to the identification of new biomarkers that can reflect tumor burden and predict its development.

44. Reevaluation of copy number variant (CNV) classifications in the clinical laboratory setting: challenges, insights, and experiences with a laboratory-initiated process

2021 ◽  
Vol 252-253 ◽  
pp. S15
Author(s):  
Denise I Quigley ◽  
Zoe K Lewis ◽  
Timothy Tidwell ◽  
Adam Clayton ◽  
Brandon Chandler ◽  
...  
Keyword(s):  
Copy Number ◽  
Clinical Laboratory ◽  
Copy Number Variant ◽  
Laboratory Setting
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