CNV-LDC: An Optimized CNV Detection Method for Low Depth of Coverage Data

Salmi, Ayyoub; Jadid, Sara El; Jamail, Ismail; Bensellak, Taoufik; Philippe, Romain; Blanquet, Véronique; Moussa, Ahmed

doi:10.5220/0006111600370042

Cited by 2 publications

(2 citation statements)

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“…A series of consecutive bases constitute a window, and the depths of the bases within the window are accumulated to obtain stable and convincing read-depth information 35,36 . Generally, the genome is partitioned into nonoverlapping sliding windows with an equal size of 100 bp as a default 28,36,62 , and the base-read depths in each window are summed as the raw "window read depth". The i th raw window read depth is denoted by R Raw,i .…”

Section: Methodsmentioning

confidence: 99%

CONY: A Bayesian procedure for detecting copy number variations from sequencing read depths

Wei

Huang

2020

Sci Rep

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copy number variations (cnVs) are genomic structural mutations consisting of abnormal numbers of fragment copies. next-generation sequencing of read-depth signals mirrors these variants. Some tools used to predict cnVs by depth have been published, but most of these tools can be applied to only a specific data type due to modeling limitations. We develop a tool for copy number variation detection by a Bayesian procedure, i.e., conY, that adopts a Bayesian hierarchical model and an efficient reversible-jump Markov chain Monte Carlo inference algorithm for whole genome sequencing of read-depth data. conY can be applied not only to individual samples for estimating the absolute number of copies but also to case-control pairs for detecting patient-specific variations. We evaluate the performance of CONY and compare CONY with competing approaches through simulations and by using experimental data from the 1000 Genomes Project. CONY outperforms the other methods in terms of accuracy in both single-sample and paired-samples analyses. in addition, conY performs well regardless of whether the data coverage is high or low. CONY is useful for detecting both absolute and relative CNVs from read-depth data sequences. The package is available at https://github.com/ weiyuchung/CONY. Copy number variations (CNVs) are genomic structural mutations consisting of abnormal numbers of deoxyribonucleic acid (DNA) section copies. CNVs were originally defined to range from one kilobasepair to several megabasepairs 1,2 and widened to include small variants that are larger than 50 basepairs in size 3,4. Currently, approximately 7 million CNVs identified in 1 million variant regions are catalogued in the Database of Genomic Variants (DGV) 5,6. Half the identified CNVs overlap with protein-coding regions, which results in gene expression changes 7. CNVs have been confirmed to play important roles in human diseases; for example, glycophorin CNVs in malaria resistance 8 , beta-defensin CNVs in Psoriasis 9,10 , CNVs in 15q11.2 for the perigenual anterior cingulate cortex in schizophrenia and Alzheimer's disease 11,12 , and some pathogenic CNVs in developmental delay, autism spectrum disorders, and various congenital malformations 13,14. Furthermore, somatic copy number aberrations have been considered to be associated with human cancers and to categorize the subtypes of cancer 15 , such as breast cancer 16,17 , lung cancer 18,19 , and colorectal cancer 20,21. Array comparative genomic hybridization 22,23 and single nucleotide polymorphism arrays 24,25 have been used to detect CNVs over the past few years; however, the boundaries of CNVs cannot be explicitly identified due to the sparse probe coverage. Recently, next-generation sequencing (NGS) 26,27 has provided a more accurate option for CNV identification and breakpoint prediction through the high-resolution analysis of sequential DNA nucleotide bases. Various strategies, including read depth 28-36 , paired-end mapping 37-40 , split read 41-43 , assembly 44-46 and integrative approaches 47-51...

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Section: Methodsmentioning

confidence: 99%

CONY: A Bayesian procedure for detecting copy number variations from sequencing read depths

Wei

Huang

2020

Sci Rep

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“…Original read files were obtained by sequencing on the HiSeq3000 platform. Sequencing files were compared with the human reference genome GRCH37/hg19 using the bowtie2 package in Linux (7). Samtools package in Linux was used to sort and make index to obtain the bam intermediate file (8).…”

Section: Low-depth Whole-genome Sequencingmentioning

confidence: 99%

Case Report: Genetic Analysis of a Small Supernumerary Marker Chromosome in a Unique Case of Mosaic Turner Syndrome

Luo

Xiao

et al. 2022

Front. Pediatr.

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BackgroundThe aim of this study was to explore the source and morphology of a small supernumerary marker chromosome (sSMC) from karyotype analysis of a patient with a unique case of mosaic Turner syndrome. The study findings will provide technical reference and genetic counseling for similar cases.Case PresentationA female patient with 46,X,+mar karyotype was diagnosed by genetic karyotype analysis. Genetic methods including fluorescence in situ hybridization (FISH) and copy number variation sequencing (CNV-seq) based on low-depth whole-genome sequencing were used to explore the source and morphology of sSMC. FISH technology showed that 56.5% of the cells were X and 43.5% of the cells were XY. CNV-seq detection found that the sSMC was chrY, implying that the patient's karyotype was mos 45,X[58.6%]/46,XY[41.4%]. Retrospective karyotype analysis indicated that the female patient's sSMC was inherited from her father's small chrY. Customized FISH probe of Yq12 microdeletion was positive, indicating that the sSMC was a del(Y)(q12). Based on the results of genetic diagnosis, the specialist doctor gave a comprehensive genetic consultation and ordered regular follow-up examinations.ConclusionsThe findings of the current study showed that the chromosome description of the unique Turner case was mos 45,X[56.5%]/46,X,del(Y)(q12)[43.5%]. FISH technology played a key role in diagnosis of mosaicism. The terminal deletion of mosaic chrY provided a scientific and an accurate explanation for masculinity failure and abnormal sexual development of the current case.

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CNV-LDC: An Optimized CNV Detection Method for Low Depth of Coverage Data

Cited by 2 publications

References 0 publications

CONY: A Bayesian procedure for detecting copy number variations from sequencing read depths

CONY: A Bayesian procedure for detecting copy number variations from sequencing read depths

Case Report: Genetic Analysis of a Small Supernumerary Marker Chromosome in a Unique Case of Mosaic Turner Syndrome

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