Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants.
paper
Cited
Public
- Authors
- Pinto, Dalila; Darvishi, Katayoon; Shi, Xinghua; Rajan, Diana; Rigler, Diane; Fitzgerald, Tom; Lionel, Anath C; Thiruvahindrapuram, Bhooma; Macdonald, Jeffrey R; Mills, Ryan; Prasad, Aparna; Noonan, Kristin; Gribble, Susan; Prigmore, Elena; Donahoe, Patricia K; Smith, Richard S; Park, Ji Hyeon; Hurles, Matthew E; Carter, Nigel P; Lee, Charles; Scherer, Stephen W; Feuk, Lars
- Year
- 2011
- Journal
- Nature biotechnology
- PMID
- 21552272
- DOI
- 10.1038/nbt.1852
- PMCID
- PMC3270583
We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with <50% concordance. Moreover, reproducibility in replicate experiments is <70% for most platforms. Nevertheless, these findings should not preclude detection of large CNVs for clinical diagnostic purposes because large CNVs with poor reproducibility are found primarily in complex genomic regions and would typically be removed by standard clinical data curation. The striking differences between CNV calls from different platforms and analytic tools highlight the importance of careful assessment of experimental design in discovery and association studies and of strict data curation and filtering in diagnostics. The CNV resource presented here allows independent data evaluation and provides a means to benchmark new algorithms.
Size distribution of CNV calls. The size distribution for the high-confidence CNV calls (that is, CNV calls made in at least two of three replicates) is shown for all combinations of algorithms (Table 1, CNV analysis tools) and platforms. Each bin represents a different range of CNV lengths and the bars show the percentage of CNVs falling into each size bin. Representative results are shown for one genotyping site only, where the average number of CNVs per sample for that site is given in parentheses. The size distribution is therefore not representative of a sample. Instead, it represents the sizes of CNV calls detected in a total of six samples. Results for all sites and further breakdown into gains-only and losses-only can be found in Supplementary Figure 4. *For Affymetrix 250K-Nsp, dChip detects on average one CNV per sample. Affy, Affymetrix; Ilmn, Illumina; AG, Agilent; BAC, bacterial artificial chromosome; cnvPart, cnvPartition; NG, NimbleGen; PCNV, PennCNV; QSNP, QuantiSNP.
CNV calling reproducibility. (a–c) Call reproducibility was evaluated by either comparing calls obtained from triplicate experiments (a,b) or by a comparison to various independent reference data sets (c). The percentage of concordant CNV calls between replicates for each combination of array, algorithm and site (a). The corresponding average number of CNVs per sample is given in b. The results for the lower-resolution arrays can be found in Supplementary Figure 8. (c) The percentage of high-confidence CNV calls for each set of results that overlaps (minimum of 50% reciprocal overlap) with data from DGV, and references 11 and 41. The DGV data were divided into array-based CNVs and sequence-based CNVs, and for the reference 11 data we independently considered a set of 8,599 validated variants as well as a subset of 4,978 CNVs that were genotyped. The poor performance of the BAC array is explained by the fact that the DGV data set was filtered so that low-resolution studies (including BAC array data) were removed. Site abbreviations: see Table 1 legend.
Reproducibility of CNV breakpoint assignments. The distances between the breakpoints for replicated CNV calls were divided into size bins for each platform, and the proportion of CNVs in each bin are plotted separately for the start (red, left) and end (blue, right) coordinates. The total number of breakpoints is given in parentheses. The data show that high-resolution platforms are highly consistent in the assignment of start and end coordinates for CNVs called across replicate experiments. Affy, Affymetrix; BAC, bacterial artificial chromosome; brkpt, breakpoint; HMS, Harvard Medical School; Ilmn, Illumina; TCAG, The Centre for Applied Genomics; WTSI, Wellcome Trust Sanger Institute.
CNV breakpoint accuracy. (a,b) The breakpoint accuracy for CNV deletions on each platform was assessed in a comparison to published sequencing data sets of nucleotide-resolution breakpoints compiled from various studies43,44 (a), or detected in the 1000 Genomes Project45,46 (b). Only a subset of platforms is included in this figure, as the lower resolution arrays did not have enough overlapping variants to make the comparison meaningful. In b, a total of 3,544 deletion breakpoints for sample NA18517 were collected from the 1000 Genomes Project and compared to the CNVs detected in each of the analyses in this study. Every row in the diagram corresponds to one of the 3,544 deletions and the color indicates whether that deletion was detected in the present study. Each row represents the distance between array versus sequencing-based breakpoints (`left' + `right' breakpoints for the same event are listed in adjacent rows). Schematic below shows sample-based comparisons between deletion breakpoints obtained with array versus sequencing methods. Gray means the deletion was not detected, whereas a color on the red-green scale is indicative of the accuracy of detected breakpoints. 1000G, 1000 Genomes Project.
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| Haplotype phasing and inheritance of copy number variants in nuclear families. | Palta P et al. | — | 2015 | → |
| Identification of rare germline copy number variations over-represented in five human cancer types. | Park RW et al. | — | 2015 | → |
| Improved Detection and Characterization of Copy Number Variations Among Diverse Pig Breeds by Array CGH. | Wang J et al. | — | 2015 | → |
| Large Autosomal Copy-Number Differences within Unselected Monozygotic Twin Pairs are Rare. | McRae AF et al. | — | 2015 | → |
| Leukocyte-specific protein 1 regulates T-cell migration in rheumatoid arthritis. | Hwang SH et al. | — | 2015 | → |
| Microdeletions of ELP4 Are Associated with Language Impairment, Autism Spectrum Disorder, and Mental Retardation. | Addis L et al. | — | 2015 | → |
| One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies. | Yuan S et al. | — | 2015 | → |
| Performance of case-control rare copy number variation annotation in classification of autism. | Engchuan W et al. | — | 2015 | → |
| Prevalence and penetrance of ZFPM2 mutations and deletions causing congenital diaphragmatic hernia. | Longoni M et al. | — | 2015 | → |
| Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing. | Tang MH et al. | — | 2015 | → |
| SG-ADVISER CNV: copy-number variant annotation and interpretation. | Erikson GA et al. | — | 2015 | → |
| The Role of Constitutional Copy Number Variants in Breast Cancer. | Walker LC et al. | — | 2015 | → |
| The variation game: Cracking complex genetic disorders with NGS and omics data. | Cui H et al. | — | 2015 | → |
| Using extended pedigrees to identify novel autism spectrum disorder (ASD) candidate genes. | Woodbury-Smith M et al. | — | 2015 | → |
| 16p11.2 600 kb Duplications confer risk for typical and atypical Rolandic epilepsy. | Reinthaler EM et al. | — | 2014 | → |
| An unbiased method for detection of genome-wide off-target effects in cell lines treated with zinc finger nucleases. | Lindsay CR et al. | — | 2014 | → |
| Associations of MYH3 gene copy number variations with transcriptional expression and growth traits in Chinese cattle. | Xu Y et al. | — | 2014 | → |
| Biological relevance of CNV calling methods using familial relatedness including monozygotic twins. | Castellani CA et al. | — | 2014 | → |
| Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. | Pinto D et al. | — | 2014 | → |
| Copy number variants and therapeutic response to antidepressant medication in major depressive disorder. | Tansey KE et al. | — | 2014 | → |
| Copy number variant study of bipolar disorder in Canadian and UK populations implicates synaptic genes. | Noor A et al. | — | 2014 | → |
| Copy number variation distribution in six monozygotic twin pairs discordant for schizophrenia. | Castellani CA et al. | — | 2014 | → |
| Copy number variation in Han Chinese individuals with autism spectrum disorder. | Gazzellone MJ et al. | — | 2014 | → |
| Copy number variation in obsessive-compulsive disorder and tourette syndrome: a cross-disorder study. | McGrath LM et al. | — | 2014 | → |
| Copy number variations among silkworms. | Zhao Q et al. | — | 2014 | → |
| Currarino Syndrome and HPE Microform Associated with a 2.7-Mb Deletion in 7q36.3 Excluding SHH Gene. | Coutton C et al. | — | 2014 | → |
| Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level. | Shin DH et al. | — | 2014 | → |
| De novo mutations in HCN1 cause early infantile epileptic encephalopathy. | Nava C et al. | — | 2014 | → |
| Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content. | Zhang H et al. | — | 2014 | → |
| Detection of monogenic disorders and chromosome aberrations by preimplantation genetic diagnosis. | Xu K et al. | — | 2014 | → |
| Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation. | Narang A et al. | — | 2014 | → |
| Focal chromosomal copy number aberrations in cancer-Needles in a genome haystack. | Krijgsman O et al. | — | 2014 | → |
| Genome-wide characterization of circulating tumor cells identifies novel prognostic genomic alterations in systemic melanoma metastasis. | Chiu CG et al. | — | 2014 | → |
| Genome-wide CNV analysis in mouse induced pluripotent stem cells reveals dosage effect of pluripotent factors on genome integrity. | Chen Y et al. | — | 2014 | → |
| Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array. | Molin AM et al. | — | 2014 | → |
| Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing. | Yi G et al. | — | 2014 | → |
| Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium. | Altmäe S et al. | — | 2014 | → |
| Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays. | Seiser EL et al. | — | 2014 | → |
| Human gene copy number variation and infectious disease. | Hollox EJ et al. | — | 2014 | → |
| Identification of risk genes for autism spectrum disorder through copy number variation analysis in Austrian families. | Egger G et al. | — | 2014 | → |
| Loss of heterozygosity at the CYP2D6 locus in breast cancer: implications for germline pharmacogenetic studies. | Goetz MP et al. | — | 2014 | → |
| Measurement of absolute copy number variation reveals association with essential hypertension. | Marques FZ et al. | — | 2014 | → |
| Modeling the altered expression levels of genes on signaling pathways in tumors as causal bayesian networks. | Neapolitan R et al. | — | 2014 | → |
| Non-random DNA fragmentation in next-generation sequencing. | Poptsova MS et al. | — | 2014 | → |
| Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia. | Mokhtar SS et al. | — | 2014 | → |
| Ohnologs are overrepresented in pathogenic copy number mutations. | McLysaght A et al. | — | 2014 | → |
| Rare de novo copy number variants in patients with congenital pulmonary atresia. | Xie L et al. | — | 2014 | → |
| Structural genomic variation as risk factor for idiopathic recurrent miscarriage. | Nagirnaja L et al. | — | 2014 | → |
| The challenges and importance of structural variation detection in livestock. | Bickhart DM et al. | — | 2014 | → |
| The complexity of genomic structural variation in neurodevelopmental disorders. | Daley M | — | 2014 | → |
| Zebrafish sex: a complicated affair. | Liew WC et al. | — | 2014 | → |
| A 1.1Mb deletion in distal 13q deletion syndrome region with congenital heart defect and postaxial polydactyly: additional support for a CHD locus at distal 13q34 region. | Yang YF et al. | — | 2013 | → |
| Advantage of using allele-specific copy numbers when testing for association in regions with common copy number variants. | Marenne G et al. | — | 2013 | → |
| Analysis of copy number variants by three detection algorithms and their association with body size in horses. | Metzger J et al. | — | 2013 | → |
| Array comparative genomic hybridization: an overview of protocols, applications, and technology trends. | Banerjee D | — | 2013 | → |
| A stochastic inference of de novo CNV detection and association test in multiplex schizophrenia families. | Wang SH et al. | — | 2013 | → |
| Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation. | Veal CD et al. | — | 2013 | → |
| Chromosomal Microarrays in Prenatal Diagnosis: Time for a Change of Policy? | Miny P et al. | — | 2013 | → |
| [Chromosomal structural variation -- an approach for multiple system atrophy]. | Yabe I et al. | — | 2013 | → |
| Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data. | Xu L et al. | — | 2013 | → |
| Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges. | Liu B et al. | — | 2013 | → |
| Copy number variation genotyping using family information. | Chu JH et al. | — | 2013 | → |
| Copy number variation in hereditary non-polyposis colorectal cancer. | Masson AL et al. | — | 2013 | → |
| Copy number variations of MICAL-L2 shaping gene expression contribute to different phenotypes of cattle. | Xu Y et al. | — | 2013 | → |
| Detecting large copy number variants using exome genotyping arrays in a large Swedish schizophrenia sample. | Szatkiewicz JP et al. | — | 2013 | → |
| Detection limits of DNA copy number alterations in heterogeneous cell populations. | Krijgsman O et al. | — | 2013 | → |
| Detection of clinically relevant copy number variants with whole-exome sequencing. | de Ligt J et al. | — | 2013 | → |
| Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. | Jiang YH et al. | — | 2013 | → |
| Determination of genomic copy number alteration emphasizing a restriction site-based strategy of genome re-sequencing. | Zheng C et al. | — | 2013 | → |
| Enhancing systems medicine beyond genotype data by dynamic patient signatures: having information and using it too. | Emmert-Streib F et al. | — | 2013 | → |
| Evaluation of calling algorithms for array-CGH. | Roy S et al. | — | 2013 | → |
| Exon-disrupting deletions of NRXN1 in idiopathic generalized epilepsy. | Møller RS et al. | — | 2013 | → |
| Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus. | Beunders G et al. | — | 2013 | → |
| Expanding probe repertoire and improving reproducibility in human genomic hybridization. | Dorman SN et al. | — | 2013 | → |
| Familial microdeletion of 17q24.3 upstream of SOX9 is associated with isolated Pierre Robin sequence due to position effect. | Amarillo IE et al. | — | 2013 | → |
| Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data. | Thieme S et al. | — | 2013 | → |
| Genome-wide copy number variation analysis in extended families and unrelated individuals characterized for musical aptitude and creativity in music. | Ukkola-Vuoti L et al. | — | 2013 | → |
| Genome-wide copy number variation study in anorectal malformations. | Wong EH et al. | — | 2013 | → |
| Germline copy number variations associated with breast cancer susceptibility in a Japanese population. | Suehiro Y et al. | — | 2013 | → |
| GStream: improving SNP and CNV coverage on genome-wide association studies. | Alonso A et al. | — | 2013 | → |
| High-resolution SNP microarray investigation of copy number variations on chromosome 18 in a control cohort. | Chia NL et al. | — | 2013 | → |
| Identification of candidate intergenic risk loci in autism spectrum disorder. | Walker S et al. | — | 2013 | → |
| Increased CNV-region deletions in mild cognitive impairment (MCI) and Alzheimer's disease (AD) subjects in the ADNI sample. | Guffanti G et al. | — | 2013 | → |
| Integrated genomic, transcriptomic, and RNA-interference analysis of genes in somatic copy number gains in pancreatic ductal adenocarcinoma. | Samuel N et al. | — | 2013 | → |
| Microarray resources for genetic and genomic studies in chicken: a review. | Gheyas AA et al. | — | 2013 | → |
| Molecular methods for genotyping complex copy number polymorphisms. | Cantsilieris S et al. | — | 2013 | → |
| ParseCNV integrative copy number variation association software with quality tracking. | Glessner JT et al. | — | 2013 | → |
| Pathogenic rare copy number variants in community-based schizophrenia suggest a potential role for clinical microarrays. | Costain G et al. | — | 2013 | → |
| Performance comparison of Affymetrix SNP6.0 and cytogenetic 2.7M whole-genome microarrays in complex cancer samples. | Bødker JS et al. | — | 2013 | → |
| Rare exonic deletions implicate the synaptic organizer Gephyrin (GPHN) in risk for autism, schizophrenia and seizures. | Lionel AC et al. | — | 2013 | → |
| Rare exonic deletions of the RBFOX1 gene increase risk of idiopathic generalized epilepsy. | Lal D et al. | — | 2013 | → |
| Short copy number variations potentially associated with tonic immobility responses in newly hatched chicks. | Abe H et al. | — | 2013 | → |
| The emerging spectrum of allelic variation in schizophrenia: current evidence and strategies for the identification and functional characterization of common and rare variants. | Mowry BJ et al. | — | 2013 | → |
| The genome-wide landscape of copy number variations in the MUSGEN study provides evidence for a founder effect in the isolated Finnish population. | Kanduri C et al. | — | 2013 | → |
| The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation. | Valsesia A et al. | — | 2013 | → |
| The role of high-throughput technologies in clinical cancer genomics. | Idris SF et al. | — | 2013 | → |
| The utility of copy number variation (CNV) in studies of hypertension-related left ventricular hypertrophy (LVH): rationale, potential and challenges. | Boonpeng H et al. | — | 2013 | → |
| Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer. | Barrett CL et al. | — | 2013 | → |
| Ultradense array CGH and discovery of micro-copy number alterations and gene fusions in the cancer genome. | Przybytkowski E et al. | — | 2013 | → |
| A discovery resource of rare copy number variations in individuals with autism spectrum disorder. | Prasad A et al. | — | 2012 | → |
| A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method. | Wang Y et al. | — | 2012 | → |
| A preliminary study of copy number variation in Tibetans. | Zhang YB et al. | — | 2012 | → |
| A survey of copy-number variation detection tools based on high-throughput sequencing data. | Xi R et al. | — | 2012 | → |
| Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. | Le Scouarnec S et al. | — | 2012 | → |
| Chromosomal variation in lymphoblastoid cell lines. | Shirley MD et al. | — | 2012 | → |
| CNVs leading to fusion transcripts in individuals with autism spectrum disorder. | Holt R et al. | — | 2012 | → |
| Copy number variation in the cattle genome. | Liu GE et al. | — | 2012 | → |
| Copy number variation of individual cattle genomes using next-generation sequencing. | Bickhart DM et al. | — | 2012 | → |
| De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia. | Kirov G et al. | — | 2012 | → |
| Detectable clonal mosaicism and its relationship to aging and cancer. | Jacobs KB et al. | — | 2012 | → |
| Detectable clonal mosaicism from birth to old age and its relationship to cancer. | Laurie CC et al. | — | 2012 | → |
| Direct-to-Consumer genetic testing: what are we talking about? | Weaver M et al. | — | 2012 | → |
| DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues. | Craig JM et al. | — | 2012 | → |
| Duplication of 8q12 encompassing CHD7 is associated with a distinct phenotype but without duane anomaly. | Luo H et al. | — | 2012 | → |
| Effect of Combining Multiple CNV Defining Algorithms on the Reliability of CNV Calls from SNP Genotyping Data. | Kim SY et al. | — | 2012 | → |
| Escaping the cut by restriction enzymes through single-strand self-annealing of host-edited 12-bp and longer synthetic palindromes. | Castro-Chavez F | — | 2012 | → |
| Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. | Hou Y et al. | — | 2012 | → |
| Genetic association studies of copy-number variation: should assignment of copy number states precede testing? | Breheny P et al. | — | 2012 | → |
| Genome-wide arrays: quality criteria and platforms to be used in routine diagnostics. | Vermeesch JR et al. | — | 2012 | → |
| Genome-wide survey of large rare copy number variants in Alzheimer's disease among Caribbean hispanics. | Ghani M et al. | — | 2012 | → |
| Genomic microarrays: a technology overview. | Brady PD et al. | — | 2012 | → |
| Germline DNA copy number variation in familial and early-onset breast cancer. | Krepischi AC et al. | — | 2012 | → |
| Human gene copy number spectra analysis in congenital heart malformations. | Tomita-Mitchell A et al. | — | 2012 | → |
| Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort. | Valsesia A et al. | — | 2012 | → |
| Identification of germline genomic copy number variation in familial pancreatic cancer. | Al-Sukhni W et al. | — | 2012 | → |
| Inheritance model introduces differential bias in CNV calls between parents and offspring. | Kim S et al. | — | 2012 | → |
| Molecular inversion probes: a novel microarray technology and its application in cancer research. | Wang Y et al. | — | 2012 | → |
| Number of rare germline CNVs and TP53 mutation types. | Silva AG et al. | — | 2012 | → |
| Rare copy number variations in adults with tetralogy of Fallot implicate novel risk gene pathways. | Silversides CK et al. | — | 2012 | → |
| Rare deletions at the neurexin 3 locus in autism spectrum disorder. | Vaags AK et al. | — | 2012 | → |
| Reconstructing DNA copy number by joint segmentation of multiple sequences. | Zhang Z et al. | — | 2012 | → |
| SHANK1 Deletions in Males with Autism Spectrum Disorder. | Sato D et al. | — | 2012 | → |
| The clinical utility of molecular karyotyping using high-resolution array-comparative genomic hybridization. | Tzetis M et al. | — | 2012 | → |
| Twins, tissue, and time: an assessment of SNPs and CNVs. | Scheet P et al. | — | 2012 | → |
| Using ERDS to infer copy-number variants in high-coverage genomes. | Zhu M et al. | — | 2012 | → |
| Using family data as a verification standard to evaluate copy number variation calling strategies for genetic association studies. | Zheng X et al. | — | 2012 | → |
| Copy number variation analysis of matched ovarian primary tumors and peritoneal metastasis. | Malek JA et al. | — | 2011 | → |
| Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms. | Haraksingh RR et al. | — | 2011 | → |
| Rare copy number variation discovery and cross-disorder comparisons identify risk genes for ADHD. | Lionel AC et al. | — | 2011 | → |
| Risk factors for autism: translating genomic discoveries into diagnostics. | Scherer SW et al. | — | 2011 | → |