ArticleNature genetics2006
Genome assembly comparison identifies structural variants in the human genome.
Article in Nature genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
72 citing papers in PubMed.
- Assembly of a high-quality Polypterus senegalus diploid genome.Genes & genomics · 2025Article
- The Evolving Role of Diagnostic Genomics in Kidney Transplantation.Kidney international reports · 2022Review
- Discovery of genomic variation across a generation.Human molecular genetics · 2021Article
- Integrative analysis of rare copy number variants and gene expression data in alopecia areata implicates an aetiological role for autophagy.Experimental dermatology · 2020Article
- Genomic Insight into the Role of lncRNA in Cancer Susceptibility.International journal of molecular sciences · 2017Review
- Genetics of Congenital Anomalies of the Kidney and Urinary Tract: The Current State of Play.International journal of molecular sciences · 2017Review
- Human inversions and their functional consequences.Briefings in functional genomics · 2015Review
- Genomic imbalances in pediatric patients with chronic kidney disease.The Journal of clinical investigation · 2015Observational
- CODEX: a normalization and copy number variation detection method for whole exome sequencing.Nucleic acids research · 2015Article
- Performance of high-throughput sequencing for the discovery of genetic variation across the complete size spectrum.G3 (Bethesda, Md.) · 2014Article
- DNA sequencing methods in human genetics and disease research.F1000prime reports · 2013Review
- Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches.Human genetics · 2013Article
- Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia?Personalized medicine · 2013Article
- Sequence assembly demystified.Nature reviews. Genetics · 2013Review
- Massive screening of copy number population-scale variation in Bos taurus genome.BMC genomics · 2013Article
- A computational method for detecting copy number variations using scale-space filtering.BMC bioinformatics · 2013Article
- Copy-number disorders are a common cause of congenital kidney malformations.American journal of human genetics · 2012Article
- DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism.Bioinformatics (Oxford, England) · 2012Article
- Revealing the missing expressed genes beyond the human reference genome by RNA-Seq.BMC genomics · 2011Article
- Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
20 authors.
Funding
Abstract
Numerous types of DNA variation exist, ranging from SNPs to larger structural alterations such as copy number variants (CNVs) and inversions. Alignment of DNA sequence from different sources has been used to identify SNPs and intermediate-sized variants (ISVs). However, only a small proportion of total heterogeneity is characterized, and little is known of the characteristics of most smaller-sized (<50 kb) variants. Here we show that genome assembly comparison is a robust approach for identification of all classes of genetic variation. Through comparison of two human assemblies (Celera's R27c compilation and the Build 35 reference sequence), we identified megabases of sequence (in the form of 13,534 putative non-SNP events) that were absent, inverted or polymorphic in one assembly. Database comparison and laboratory experimentation further demonstrated overlap or validation for 240 variable regions and confirmed >1.5 million SNPs. Some differences were simple insertions and deletions, but in regions containing CNVs, segmental duplication and repetitive DNA, they were more complex. Our results uncover substantial undescribed variation in humans, highlighting the need for comprehensive annotation strategies to fully interpret genome scanning and personalized sequencing projects.
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