Genome structural variation discovery and genotyping

Alkan, Can; Coe, Bradley P.; Eichler, Evan E.

doi:10.1038/nrg2958

Cited by 1,630Genomic variations and chromosomal abnormalitiesGenome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

Genome structural variation discovery and genotyping

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Alkan, Can, Coe, Bradley P., Eichler, Evan E.·2011·Nature Reviews Genetics

DOI 10.1038/nrg2958PMC PMC4108431

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Abstract

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.

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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.
“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]
The Sequence assembly section (page unavailable) says accurate characterization of structural variation depends on sufficiently accurate reads and high-quality assembly. The Array CGH section (page unavailable) describes variation among individuals and difficulty accurately assessing the proportion of the genome altered. Neither passage supports the claim about determining genome weight or relative GC content. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Human genetic diversity ranges from single-nucleotide variation to large chromosomal events.
“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]
Current genotyping platforms and CNV discovery algorithms can genotype about 1,000 common copy-number polymorphisms and discover additional novel CNVs, including rare or individual-specific mutations.
“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

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CGHcall: calling aberrations for array CGH tumor profiles
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Systematic assessment of copy number variant detection via genome-wide SNP genotyping
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Evolutionary toggling of the MAPT 17q21.31 inversion region
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Taking qPCR to a higher level: analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution
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Microarray‐based comparative genomic hybridization and its applications in human genetics
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Detecting copy number variation with mated short readsPreprint
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CYP2D6 genotyping strategy based on gene copy number determination by TaqMan real-rime PCR
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Characterization of missing human genome sequences and copy-number polymorphic insertions
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MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions
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Large multi-chromosomal duplications encompass many members of the olfactory receptor gene family in the human genome
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BAC microarray analysis of 15q11–q13 rearrangements and the impact of segmental duplications
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Genome-wide Copy Number Profiling on High-density Bacterial Artificial Chromosomes, Single-nucleotide Polymorphisms, and Oligonucleotide Microarrays: A Platform Comparison based on Statistical Power Analysis
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Public data archives for genomic structural variation
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A Comparison of DNA Copy Number Profiling Platforms
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Human genome: Genomes by the thousand
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Robust quantification of the SMN gene copy number by real-time TaqMan PCR
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Direct determination of haplotypes from single DNA molecules
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Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma
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High resolution oligonucleotide CGH using DNA from archived prostate tissue
Paris, P. L., Sridharan, S., Scheffer-Wong, A., Tsalenko, A., Bruhn, L., & Collins, C. C. (2007) · The Prostate · doi:10.1002/pros.20632 · Cited by 29 · see citing works
FACADE : a fast and sensitive algorithm for the segmentation and calling of high resolution array CGH data
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MoGUL: Detecting Common Insertions and Deletions in a Population
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Normalized, Segmented or Called aCGH Data?
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Normalized, segmented or called aCGH data?
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Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes
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Targeted interrogation of copy number variation using SCIMMkit
Zerr, T., Cooper, G. M., Eichler, E. E., & Nickerson, D. A. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp606 · Cited by 8 · see citing works
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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
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Exome sequencing as a tool for Mendelian disease gene discovery
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Accurate detection of complex structural variations using single-molecule sequencing
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Genetic architectures of psychiatric disorders: the emerging picture and its implications
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Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
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CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics
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The evolutionary origin of orphan genes
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Structural variation in the 3D genome
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De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly
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The genetics of asthma and allergic disease: a 21st century perspective
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Phenotypic impact of genomic structural variation: insights from and for human disease
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Gene duplication as a mechanism of genomic adaptation to a changing environment
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Piercing the dark matter: bioinformatics of long-range sequencing and mapping
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Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel linesPreprint
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Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives
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SpeedSeq: ultra-fast personal genome analysis and interpretation
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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
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Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
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The Human Pangenome Project: a global resource to map genomic diversity
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The impact of structural variation on human gene expression
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High Yield of RNA Sequencing for Targetable Kinase Fusions in Lung Adenocarcinomas with No Mitogenic Driver Alteration Detected by DNA Sequencing and Low Tumor Mutation Burden
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Genetic architecture: the shape of the genetic contribution to human traits and disease
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Integrative detection and analysis of structural variation in cancer genomes
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New insights into the generation and role of de novo mutations in health and disease
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The Genetic Landscapes of Autism Spectrum Disorders
Huguet, G., Ey, E., & Bourgeron, T. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153431 · Cited by 447 · see citing works
Diversity within Species: Interpreting Strains in Microbiomes
Van Rossum, T., Ferretti, P., Maistrenko, O. M., & Bork, P. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0368-1 · Cited by 441 · see citing works
Long-Read Sequencing Emerging in Medical Genetics
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Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage
Chakraborty, M., Baldwin-Brown, J. G., Long, A. D., & Emerson, J. J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw654 · Cited by 442 · see citing works
Long-read-based human genomic structural variation detection with cuteSV
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The million mutation project: A new approach to genetics in Caenorhabditis elegansPreprint
Thompson, O. A., Edgley, M. L., Strasbourger, P., Flibotte, S., Ewing, B., Adair, R., Au, V., Chaudhry, I., Fernando, L., Hutter, H., et al. (2013) · Genome Research · doi:10.1101/gr.157651.113 · Cited by 388 · see citing works
Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing
Qi, X., Li, M., Xie, M., Liu, X., Ni, M., Shao, G., Song, C., Yim, A. K., Tao, Y., Wong, F., et al. (2014) · Nature Communications · doi:10.1038/ncomms5340 · Cited by 409 · see citing works
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
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Unravelling the complexity of metastasis — molecular understanding and targeted therapies
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Authors: Alkan, C., Coe, B. P., & Eichler, E. E.
Affiliations: University of Washington (US)
Howard Hughes Medical Institute (US)
Corresponding author: Eichler, Evan E.
ORCID: Alkan, Can
Coe, Bradley P.
Eichler, Evan E.
Venue: Nature Reviews Genetics
Publisher: Springer Science and Business Media LLC
Published: 2011-03-01
Volume: 12
Issue: 5
Pages: 363-376
ISSN: 1471-0056 (ISSN-L)
1471-0064
DOI: 10.1038/nrg2958
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

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