ArticleMolecular genetics & genomic medicine2020
Genome sequencing in cytogenetics: Comparison of short-read and linked-read approaches for germline structural variant detection and characterization.
Article in Molecular genetics & genomic medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Genome sequencing for the diagnosis of intellectual disability as a paradigm for rare diseases in the French healthcare setting: the prospective DEFIDIAG study.Genome medicine · 2025Trial
- CYTO-SV-ML: A Machine Learning Tool for Cytogenetic Structural Variant Analysis in Somatic Cell Type Using Genome Sequences.Life (Basel, Switzerland) · 2025Article
- Review
- Haplotype information of large neuromuscular disease genes provided by linked-read sequencing has a potential to increase diagnostic yield.Scientific reports · 2024Article
- Cytogenomic Characterization of a Novel de novo Balanced Reciprocal Translocation t(1;12) by Genome Sequencing Leading to Fusion Gene Formation ofMolecular syndromology · 2022Article
- Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing.Scientific reports · 2021Article
- Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective.Animals : an open access journal from MDPI · 2021Review
- Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma.Cancers · 2021Article
- A BBS1 SVA F retrotransposon insertion is a frequent cause of Bardet-Biedl syndrome.Clinical genetics · 2021Article
- Article
- Using short read sequencing to characterise balanced reciprocal translocations in pigs.BMC genomics · 2020Article
- Genome sequencing in cytogenetics: Comparison of short-read and linked-read approaches for germline structural variant detection and characterization.Molecular genetics & genomic medicine · 2020Article
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31 authors.
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Abstract
backgroundStructural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base-pair resolution, but the use of short-read sequencing is limited by repetitive sequences, and long-read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked-reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short-read to linked-read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short-read WGS.
methodsWe included 13 patients carrying various SVs. Whole genome analyses were performed using paired-end HiSeq X sequencing with (linked-read strategy) or without (short-read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short-read strategy and LongRanger for long-read strategy. Variant interpretations were first blinded.
resultsThe short-read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked-read strategy identified 10/13 SVs, including one (patient 7) missed by the short-read strategy.
conclusionIn conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV.
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