The DOI matches its Crossref record; 120 of the 121 references it cites were found in a registry or an index.
Genome structural variation discovery and genotyping
Open accessAbstract
Comparisons of human genomes show that more base pairs are altered as a result of structural variation - including copy number variation - than as a result of point mutations. Here we review advances and challenges in the discovery and genotyping of structural variation. The recent application of massively parallel sequencing methods has complemented microarray-based methods and has led to an exponential increase in the discovery of smaller structural-variation events. Some global discovery biases remain, but the integration of experimental and computational approaches is proving fruitful for accurate characterization of the copy, content and structure of variable regions. We argue that the long-term goal should be routine, cost-effective and high quality de novo assembly of human genomes to comprehensively assess all classes of structural variation.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Determination of the length, weight and relative GC content of genome is subjected to the accuracy of the genome assembly and to the variability existing among individuals [41].”
From On the length, weight and GC content of the human genome (2019) · cites this paper as [41]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“However, the human genetic diversity ranges from the single-nucleotide variation to large chromosomal events [41, 42].”
From On the length, weight and GC content of the human genome (2019) · cites this paper as [41]
In the citing paper
“Current genotyping platforms and CNV discovery algorithms enable the genotyping of ~1000 common copy number polymorphisms (CNPs) and the discovery of additional “novel” CNVs, including mutations that are rare or unique to an individual (Alkan et al., 2011).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Alkan et al., 2011
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,587
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
Global variation in copy number in the human genome
Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., et al. (2006) · Nature · doi:10.1038/nature05329 · Cited by 4,377
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
ABySS: A parallel assembler for short read sequence dataPreprint
Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M., & Birol, İ. (2009) · Genome Research · doi:10.1101/gr.089532.108 · Cited by 3,658
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926
Detection of large-scale variation in the human genome
Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892
Miller, D. T., Adam, M. P., Aradhya, S., Biesecker, L. G., Brothman, A. R., Carter, N. P., Church, D. M., Crolla, J. A., Eichler, E. E., Epstein, C. J., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.04.006 · Cited by 2,882
Self-citationStrong association of de novo copy number mutations with autism
Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., et al. (2007) · Science · doi:10.1126/science.1138659 · Cited by 2,795
Schouten, J. P. (2002) · Nucleic Acids Research · doi:10.1093/nar/gnf056 · Cited by 2,705
Flagged first, then by citations
1 of the 121 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chin, C.-S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2474 · Cited by 4,029
Self-citationAn integrated map of structural variation in 2,504 human genomes
Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354
Self-citationRepetitive DNA and next-generation sequencing: computational challenges and solutions
Treangen, T. J., & Salzberg, S. L. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3117 · Cited by 1,795
Exome sequencing as a tool for Mendelian disease gene discovery
Bamshad, M. J., Ng, S. B. H., Bigham, A. W., Tabor, H. K., Emond, M. J., Nickerson, D. A., & Shendure, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3031 · Cited by 1,744
Accurate detection of complex structural variations using single-molecule sequencing
Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., & Schatz, M. C. (2018) · Nature Methods · doi:10.1038/s41592-018-0001-7 · Cited by 1,601
Metadata
- Authors
- Alkan, C., Coe, B. P., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eichler, Evan E.
- Venue
- Nature Reviews Genetics
- Published
- 2011-03-01
- Volume
- 12
- Issue
- 5
- Pages
- 363-376
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC4108431
- OpenAlex
- W2083870688
- Cited by
- 1,630
- References
- 121
- Citations by year
- 2026: 67 · 2025: 129 · 2024: 100 · 2023: 81 · 2022: 94 · 2021: 104 · 2020: 148 · 2019: 122 · 2018: 132 · 2017: 102 · 2016: 93 · 2015: 108 · 2014: 107 · 2013: 108 · 2012: 89
- FWCI
- 11.82
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- Wellcome Trust
- Canadian Institutes of Health Research
- National Human Genome Research Institute (P01HG004120)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- structural variants, copy number variation, structural variant genotyping, structural variant calling, next-generation sequencing, de novo genome assembly, human genome, complex traits
- MeSH terms
- Genotype, Humans, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, DNA Copy Number Variations, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
