ArticleGenome research2011
Simultaneous structural variation discovery among multiple paired-end sequenced genomes.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Efficient transgenic maize (Zea Mays L.) detection using low-depth next-generation sequencing.Scientific reports · 2025Article
- Blackbird: structural variant detection using synthetic and low-coverage long-reads.Bioinformatics advances · 2025Article
- Efficient identification of genomic insertions and flanking regions through whole-genome sequencing in three transgenic soybean events.Transgenic research · 2021Article
- CNV-MEANN: A Neural Network and Mind Evolutionary Algorithm-Based Detection of Copy Number Variations From Next-Generation Sequencing Data.Frontiers in genetics · 2021Article
- CONY: A Bayesian procedure for detecting copy number variations from sequencing read depths.Scientific reports · 2020Article
- Graph Traversal Edit Distance and Extensions.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Meltos: multi-sample tumor phylogeny reconstruction for structural variants.Bioinformatics (Oxford, England) · 2020Article
- Article
- Discovery of tandem and interspersed segmental duplications using high-throughput sequencing.Bioinformatics (Oxford, England) · 2019Article
- Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software.Nature communications · 2019Article
- Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine.Science China. Life sciences · 2019Review
- Efficient genome-wide genotyping strategies and data integration in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Review
- Reconstructing cancer karyotypes from short read data: the half empty and half full glass.BMC bioinformatics · 2017Article
- Article
- Molecular Approaches for High Throughput Detection and Quantification of Genetically Modified Crops: A Review.Frontiers in plant science · 2017Review
- PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.BMC bioinformatics · 2016Article
- Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data.Briefings in bioinformatics · 2016Article
- CLASS2: accurate and efficient splice variant annotation from RNA-seq reads.Nucleic acids research · 2016Article
- Joint detection of copy number variations in parent-offspring trios.Bioinformatics (Oxford, England) · 2016Article
- Identification of large-scale genomic variation in cancer genomes using in silico reference models.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
With the increasing popularity of whole-genome shotgun sequencing (WGSS) via high-throughput sequencing technologies, it is becoming highly desirable to perform comparative studies involving multiple individuals (from a specific population, race, or a group sharing a particular phenotype). The conventional approach for a comparative genome variation study involves two key steps: (1) each paired-end high-throughput sequenced genome is compared with a reference genome and its (structural) differences are identified; (2) the lists of structural variants in each genome are compared against each other. In this study we propose to move away from this two-step approach to a novel one in which all genomes are compared with the reference genome simultaneously for obtaining much higher accuracy in structural variation detection. For this purpose, we introduce the maximum parsimony-based simultaneous structural variation discovery problem for a set of high-throughput sequenced genomes and provide efficient algorithms to solve it. We compare the proposed framework with the conventional framework, on the genomes of the Yoruban mother-father-child trio, as well as the CEU trio of European ancestry (both sequenced by Illumina platforms). We observed that the conventional framework predicts an unexpectedly high number of de novo variations in the child in comparison to the parents and misses some of the known variations. Our proposed framework, on the other hand, not only significantly reduces the number of incorrectly predicted de novo variations but also predicts more of the known (true) variations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.