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. 2019 Jul 16;20(Suppl 8):545.
doi: 10.1186/s12864-019-5866-z.

A clinically validated whole genome pipeline for structural variant detection and analysis

Nir Neerman  1 , Gregory Faust  1 , Naomi Meeks  1 , Shira Modai  1 , Limor Kalfon  2 , Tzipora Falik-Zaccai  2   3 , Alexander Kaplun  4
Affiliations

A clinically validated whole genome pipeline for structural variant detection and analysis

Nir Neerman et al. BMC Genomics. .

Abstract

Background: With the continuing decrease in cost of whole genome sequencing (WGS), we have already approached the point of inflection where WGS testing has become economically feasible, facilitating broader access to the benefits that are helping to define WGS as the new diagnostic standard. WGS provides unique opportunities for detection of structural variants; however, such analyses, despite being recognized by the research community, have not previously made their way into routine clinical practice.

Results: We have developed a clinically validated pipeline for highly specific and sensitive detection of structural variants basing on 30X PCR-free WGS. Using a combination of breakpoint analysis of split and discordant reads, and read depth analysis, the pipeline identifies structural variants down to single base pair resolution. False positives are minimized using calculations for loss of heterozygosity and bi-modal heterozygous variant allele frequencies to enhance heterozygous deletion and duplication detection respectively. Compound and potential compound combinations of structural variants and small sequence changes are automatically detected. To facilitate clinical interpretation, identified variants are annotated with phenotype information derived from HGMD Professional and population allele frequencies derived from public and Variantyx allele frequency databases. Single base pair resolution enables easy visual inspection of potentially causal variants using the IGV genome browser as well as easy biochemical validation via PCR. Analytical and clinical sensitivity and specificity of the pipeline has been validated using analysis of Genome in a Bottle reference genomes and known positive samples confirmed by orthogonal sequencing technologies.

Conclusion: Consistent read depth of PCR-free WGS enables reliable detection of structural variants of any size. Annotation both on gene and variant level allows clinicians to match reported patient phenotype with detected variants and confidently report causative finding in all clinical cases used for validation.

Keywords: Break point; CNV; Clinical validation; Deletion; Diagnostic console; Duplication; Pipeline; Structural variants; WGS; Whole genome sequencing.

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Conflict of interest statement

NN, GF, NM, SM and AK are affiliated with Variantyx Inc.

Figures

Fig. 1
Fig. 1
SV component of Variantyx Genomic Intelligence WGS analysis pipeline
Fig. 2
Fig. 2
Ratio of balanced (between 40 and 60%) out of total overlapping SNVs is shifted in case of heterozygous duplications
Fig. 3
Fig. 3
Structural variant annotation on variant and gene level as presented in Diagnostic Console
Fig. 4
Fig. 4
Structural variant filtration in Diagnostic Console
See this image and copyright information in PMC

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References

    1. Jacobs PA, Browne C, Gregson N, et al. Estimates of the frequency of chromosome abnormalities detectable in unselected newborns using moderate levels of banding. J Med Genet. 1992;29:103–108. doi: 10.1136/jmg.29.2.103. - DOI - PMC - PubMed
    1. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010;86:749–764. doi: 10.1016/j.ajhg.2010.04.006. - DOI - PMC - PubMed
    1. Pang AW, MacDonald JR, Pinto D, Wei J, Rafiq MA, Conrad DF, Park H, Hurles ME, Lee C, Venter JC. Towards a comprehensive structural variation map of an individual human genome. Genome Biol. 2010;11:R52. doi: 10.1186/gb-2010-11-5-r52. - DOI - PMC - PubMed
    1. Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. 1000 genomes project consortium a global reference for human genetic variation. Nature. 2015;526:68–74. doi: 10.1038/nature15393. - DOI - PMC - PubMed
    1. Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324. - DOI - PMC - PubMed

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