Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches.

paper Cited Public

Authors: Abel, Haley J; Duncavage, Eric J
Year: 2013
Journal: Cancer genetics
PMID: 24405614
DOI: 10.1016/j.cancergen.2013.11.002
PMCID: PMC4441822

Figure 1

Identification of translocations from discordant paired-end reads. (A) In this example, a t(4;11) translocation is identified by discordant paired-end reads. Read pairs are first identified, in which one end maps to the targeted region (in this case the MLL gene on 11q23) and the other end maps to a different chromosome. (B) Discordant paired-end ead methods are subject to high false-positive rates due to sequence-mapping errors and repeat regions in the genome. Most translocation identification software employs filtering criteria to reduce the number of false-positive calls.

Figure 2

CNV by DOC analysis. In this example, CNV is called by first obtaining the DOC for every position in the targeted sequencing region. Next, DOC data must be normalized, which can be accomplished by a number of approaches, including comparing to paired normal samples (in the case of cancer), pooled normal controls, or the mean sample coverage. Once coverage is normalized, regions of constant CNV are identified, and CNV calls are then made using a variety of probabilistic models.

Figure 3

Methods for indel detection. (A) In this example, a small insertion is identified by alignment-based calling methods. Such insertions are generally identified during initial read mapping and alignment and are evaluated by indel detection programs using different models to exclude false-positive results due to sequencing or read mapping errors. (B) A medium-sized insertion is identified by split read mapping methods. In this example, an insertion (red) present in the sequenced DNA is detected by first identifying paired-end reads in which one end maps and the other (containing the inserted sequence) does not. The inserted sequence is reconstructed from the overlapping, unmapped single-end reads. (C) An insertion detected by paired-end methods. In this example, the sequenced DNA contains an insertion and read pairs mapping to the flanking normal reference sequence show a shorter than expected distance between ends, allowing for an insertion to be inferred.

#	Section	Preview
0	Introduction	The detection of structural DNA variation has long played a role in the diagnosis of cancer and…
1	Introduction	clinically relevant events such as the FIP1L1-PDGFRA deletion on chromosome 4q12 in myeloid…
2	Introduction	Next generation sequencing (NGS), often referred to as massively paralleled sequencing, is a…
3	Introduction	NGS-based diagnostics are rapidly becoming part of the clinical genomic testing and are now…
4	Introduction	Here we review methods for the identification of DNA structural variation by NGS, with particular…
5	Introduction — NGS informatics	Algorithms for detection of structural variation from NGS data rely on one or more of the following:…
6	Introduction — NGS informatics	The performance of any method for detection of structural variation depends critically on the type…
7	Introduction — Detection of translocations and inversions	Many algorithms, including BreakDancer, Hydra, PEMer, and VariationHunter, for the detection of…
8	Introduction — Detection of translocations and inversions	generated, tend to occur in regions with repetitive elements, such as tandem duplications and…
9	Introduction — Detection of translocations and inversions	In order to avoid the high false-positive rates inherent to most paired-read approaches, and to…
10	Introduction — Detection of translocations and inversions	These soft-clipped reads often indicate reads with split mappings and so can be used to localize…
11	Introduction — Detection of copy number variants	Copy number variants are defined as stretches of DNA, longer than a kilobase, that are present in…
12	Introduction — Detection of copy number variants	In whole genome sequence data, large deletions are readily detected by the same methods as…
13	Introduction — Detection of copy number variants	Discordant paired-end and split-read methods will generally not perform well for CNV detection from…
14	Introduction — Detection of copy number variants	Algorithms such as event-wise testing (EWT) for CNV detection from whole genome sequence data do not…
15	Introduction — Detection of copy number variants	Although methods for CNV detection with no control sample must explicitly account for GC bias, other…
16	Introduction — Detection of copy number variants	Detection of CNV from exome or targeted-capture sequence data presents unique challenges due to the…
17	Introduction — Detection of copy number variants	a similar strategy, first denoising the coverage ratio using a discrete wavelet transform, and then…
18	Introduction — Detection of copy number variants	An additional category of CNV detection algorithms, designed to detect sporadic CNVs from population…
19	Introduction — Detection of insertions and deletions	Indels are common in the human genome and contribute to genetic diversity and human disease…

Citation	PMID	DOI	Status
Abel, HJ et al., Bioinformatics, 2010, SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next generation sequence data.	20876606	10.1093/bioinformatics/btq528	Cited
Abyzov, A et al., Genome Res, 2011, CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.	21324876	10.1101/gr.114876.110	Cited
Albers, CA et al., Genome Res, 2011, Dindel: accurate indel calls from short-read data.	20980555	10.1101/gr.112326.110	Cited
Amarasinghe, KC et al., BMC Bioinformatics, 2013, CoNVEX: copy number variation estimation in exome sequencing data using HMM.	23368785	10.1186/1471-2105-14-S2-S2	Cited
Bentley, DR et al., Nature, 2008, Accurate whole human genome sequencing using reversible terminator chemistry.	18987734	10.1038/nature07517	Cited
Brodeur, GM et al., Science, 1984, Amplification of N-myc in untreated human neuroblastomas correlates with advanced disease stage.	6719137	10.1126/science.6719137	Cited
Chen, K et al., Nat Methods, 2009, BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.	19668202	10.1038/nmeth.1363	Cited
Chiang, DY et al., Nat Methods, 2009, High-resolution mapping of copy-number alterations with massively parallel sequencing.	19043412	10.1038/nmeth.1276	Cited
Clark, MJ et al., Nat Biotechnol, 2011, Performance comparison of exome DNA sequencing technologies.	21947028	10.1038/nbt.1975	Cited
Cools, J et al., N Engl J Med, 2003, A tyrosine kinase created by fusion of the PDGFRA and FIP1L1 genes as a therapeutic target of imatinib in idiopathic hypereosinophilic syndrome.	12660384	10.1056/NEJMoa025217	Cited
de Jesus Marques-Salles, T et al., Cancer Genet Cytogenet, 2009, A new chromosomal three-way rearrangement involving MLL masked by a t(9;19)(p11;p13) in an infant with acute myeloid leukemia.	19167614	10.1016/j.cancergencyto.2008.10.009	Cited
DePristo, MA et al., Nat Genet, 2011, A framework for variation discovery and genotyping using next generation DNA sequencing data.	21478889	10.1038/ng.806	Cited
Duncavage, EJ et al., Mod Pathol, 2012, Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia.	22425908	10.1038/modpathol.2012.29	Cited
Ellis, MJ et al., Nature, 2012, Whole-genome analysis informs breast cancer response to aromatase inhibition.	22722193	10.1038/nature11143	Cited
Falini, B et al., N Engl J Med, 2005, Cytoplasmic nucleophosmin in acute myelogenous leukemia with a normal karyotype.	15659725	10.1056/NEJMoa041974	Cited
Feuk, L et al., Nat Rev Genet, 2006, Structural variation in the human genome.	16418744	10.1038/nrg1767	Cited
Freeman, J et al., Genome Res, 2006, Copy number variation: new insights in genome diversity.	16809666	10.1101/gr.3677206	Cited
Fromer, M et al., Am J Hum Genet, 2012, Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth.	23040492	10.1016/j.ajhg.2012.08.005	Cited
Govindan, R et al., Cell, 2012, Genomic landscape of non-small cell lung cancer in smokers and never-smokers.	22980976	10.1016/j.cell.2012.08.024	Cited
Grimm, D et al., BMC Genomics, 2013, Accurate indel prediction using paired-end short reads.	23442375	10.1186/1471-2164-14-132	Cited
Hamada, M et al., Bioinformatics, 2011, Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection.	21976422	10.1093/bioinformatics/btr537	Cited
Hormozdiari, F et al., Bioinformatics, 2010, Next generation VariationHunter: combinatorial algorithms for transposon insertion discovery.	20529927	10.1093/bioinformatics/btq216	Cited
Ivakhno, S et al., Bioinformatics, 2011, CNAsegda novel framework for identification of copy number changes in cancer from second-generation sequencing data.	20966003	10.1093/bioinformatics/btq587	Cited
Koboldt, DC et al., Genome Res, 2012, VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.	22300766	10.1101/gr.129684.111	Cited
Korbel, JO et al., Genome Biol, 2009, PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.	19236709	10.1186/gb-2009-10-2-r23	Cited
Krumm, N et al., Genome Res, 2012, Copy number variation detection and genotyping from exome sequence data.	22585873	10.1101/gr.138115.112	Cited
Lejeune, J et al., C R Hebd Seances Acad Sci, 1959, Study of somatic chromosomes from 9 mongoloid children [in French].	13639368	—	Cited
Li, H et al., Bioinformatics, 2009, The Sequence Alignment/Map format and SAMtools.	19505943	10.1093/bioinformatics/btp352	Cited
Li, H et al., Bioinformatics, Fast and accurate long-read alignment with Burrows-Wheeler transform.	20080505	10.1093/bioinformatics/btp698	Cited
Li, H et al., Genome Res, 2008, Mapping short DNA sequencing reads and calling variants using mapping quality scores.	18714091	10.1101/gr.078212.108	Cited
Li, J et al., Bioinformatics, 2012, CONTRA: copy number analysis for targeted resequencing.	22474122	10.1093/bioinformatics/bts146	Cited
Mardis, ER et al., N Engl J Med, 2009, Recurring mutations found by sequencing an acute myeloid leukemia genome.	19657110	10.1056/NEJMoa0903840	Cited
Mardis, ER, Annu Rev Anal Chem (Palo Alto Calif), 2013, Next generation sequencing platforms.	23560931	10.1146/annurev-anchem-062012-092628	Cited
Mardis, ER, Genome Med, 2009, New strategies and emerging technologies for massively parallel sequencing: applications in medical research.	19435481	10.1186/gm40	Cited
Medvedev, P et al., Nat Methods, 2009, Computational methods for discovering structural variation with next generation sequencing.	19844226	10.1038/nmeth.1374	Cited
Nakao, M et al., Leukemia, 1996, Internal tandem duplication of the flt3 gene found in acute myeloid leukemia.	8946930	—	Cited
Nord, AS et al., BMC Genomics, 2011, Accurate and exact CNV identification from targeted high-throughput sequence data.	21486468	10.1186/1471-2164-12-184	Cited
O'Rawe, J et al., Genome Med, 2013, Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.	23537139	10.1186/gm432	Cited
Olshen, AB et al., Biostatistics, 2004, Circular binary segmentation for the analysis of array-based DNA copy number data.	15475419	10.1093/biostatistics/kxh008	Cited
Paschka, P et al., J Clin Oncol, 2006, Adverse prognostic significance of KIT mutations in adult acute myeloid leukemia with inv(16) and t(8;21): a Cancer and Leukemia Group B. Study.	16921041	10.1200/JCO.2006.06.9500	Cited
Pritchard, CC et al., J Mol Diagn, 2012, ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing.	22658618	10.1016/j.jmoldx.2012.03.002	Cited
Quinlan, AR et al., Genome Res, 2010, Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.	20308636	10.1101/gr.102970.109	Cited
Rowley, JD, Nature, 1973, Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining.	4126434	10.1038/243290a0	Cited
Sathirapongsasuti, JF et al., Bioinformatics, 2011, Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.	21828086	10.1093/bioinformatics/btr462	Cited
Sebat, J et al., Science, 2007, Strong association of de novo copy number mutations with autism.	17363630	10.1126/science.1138659	Cited
Sequist, LV et al., J Clin Oncol, 2008, First-line gefitinib in patients with advanced non-small-cell lung cancer harboring somatic EGFR mutations.	18458038	10.1200/JCO.2007.14.8494	Cited
Sindi, SS et al., Genome Biol, An integrative probabilistic model for identification of structural variation in sequencing data.	22452995	10.1186/gb-2012-13-3-r22	Cited
Soda, M et al., Nature, 2007, Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer.	17625570	10.1038/nature05945	Cited
Spencer, DH et al., J Mol Diagn, 2012, Detection of FLT3 internal tandem duplication in targeted, short-read-length, next generation sequencing data.	23159595	10.1016/j.jmoldx.2012.08.001	Cited
Suzuki, S et al., BMC Bioinformatics, 2011, ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.	22373054	10.1186/1471-2105-12-S14-S7	Cited
Vignot, S et al., J Clin Oncol, 2013, Next generation sequencing reveals high concordance of recurrent somatic alterations between primary tumor and metastases from patients with non-small-cell lung cancer.	23630207	10.1200/JCO.2012.47.7737	Cited
von Deimling, A et al., Cancer Res, 1992, Evidence for a tumor suppressor gene on chromosome 19q associated with human astrocytomas, oligodendrogliomas, and mixed gliomas.	1353411	—	Cited
Walsh, T et al., Science, 2008, Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia.	18369103	10.1126/science.1155174	Cited
Walter, MJ et al., N Engl J Med, 2012, Clonal architecture of secondary acute myeloid leukemia.	22417201	10.1056/NEJMoa1106968	Cited
Wang, J et al., Nat Methods, CREST maps somatic structural variation in cancer genomes with base-pair resolution.	21666668	10.1038/nmeth.1628	Cited
Welch, JS et al., JAMA, 2011, Use of whole-genome sequencing to diagnose a cryptic fusion oncogene.	21505136	10.1001/jama.2011.497	Cited
Wiltgen, M et al., Hematology, 2007, DNA microarray analysis: principles and clinical impact.	17654053	10.1080/10245330701283967	Cited
Worthey, EA et al., Genet Med, 2010, Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease.	21173700	10.1097/GIM.0b013e3182088158	Cited
Xie, C et al., BMC Bioinformatics, 2009, CNV-seq, a new method to detect copy number variation using high-throughput sequencing.	19267900	10.1186/1471-2105-10-80	Cited
Ye, K et al., Bioinformatics, 2009, Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.	19561018	10.1093/bioinformatics/btp394	Cited
Yoon, S et al., Genome Res, 2009, Sensitive and accurate detection of copy number variants using read depth of coverage.	19657104	10.1101/gr.092981.109	Cited
Zhang, ZD et al., BMC Genomics, 2011, Identification of genomic indels and structural variations using split reads.	21787423	10.1186/1471-2164-12-375	Cited
Zhou, X et al., Cancer Genet Cytogenet, 2005, Progress in concurrent analysis of loss of heterozygosity and comparative genomic hybridization utilizing high density single nucleotide polymorphism arrays.	15860358	10.1016/j.cancergencyto.2004.09.014	Cited

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Molecular diagnostics in soft tissue sarcomas and gastrointestinal stromal tumors.	Smith SM et al.	—	2015	→
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ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.	Yang R et al.	—	2015	→
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Detection of gene rearrangements in targeted clinical next-generation sequencing.	Abel HJ et al.	—	2014	→
Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing.	Suzuki T et al.	—	2014	→