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Statistical aspects of discerning indel-type structural variation via DNA sequence alignment.

Wendl MC, Wilson RK - BMC Genomics (2009)

Bottom Line: Conversely, no significant improvement would be realized in lowering fosmid variances beyond current levels.Detection power is examined under a straightforward alternative hypothesis and found to be generally acceptable.At 1% risk, many designs will leave a significant gap in the 100 to 200 bp neighborhood, requiring unacceptably high redundancies to compensate.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Genome Center and Department of Genetics, Washington University, St Louis, MO 63108, USA. mwendl@wustl.edu

ABSTRACT

Background: Structural variations in the form of DNA insertions and deletions are an important aspect of human genetics and especially relevant to medical disorders. Investigations have shown that such events can be detected via tell-tale discrepancies in the aligned lengths of paired-end DNA sequencing reads. Quantitative aspects underlying this method remain poorly understood, despite its importance and conceptual simplicity. We report the statistical theory characterizing the length-discrepancy scheme for Gaussian libraries, including coverage-related effects that preceding models are unable to account for.

Results: Deletion and insertion statistics both depend heavily on physical coverage, but otherwise differ dramatically, refuting a commonly held doctrine of symmetry. Specifically, coverage restrictions render insertions much more difficult to capture. Increased read length has the counterintuitive effect of worsening insertion detection characteristics of short inserts. Variance in library insert length is also a critical factor here and should be minimized to the greatest degree possible. Conversely, no significant improvement would be realized in lowering fosmid variances beyond current levels. Detection power is examined under a straightforward alternative hypothesis and found to be generally acceptable. We also consider the proposition of characterizing variation over the entire spectrum of variant sizes under constant risk of false-positive errors. At 1% risk, many designs will leave a significant gap in the 100 to 200 bp neighborhood, requiring unacceptably high redundancies to compensate. We show that a few modifications largely close this gap and we give a few examples of feasible spectrum-covering designs.

Conclusion: The theory resolves several outstanding issues and furnishes a general methodology for designing future projects from the standpoint of a spectrum-wide constant risk.

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Heterozygous ISV and DSV false-positive trends for 250 bp Illumina GA inserts and 40 kb fosmids (Table 2) for selected values of physical coverage (ρ = N λ/G).
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Figure 2: Heterozygous ISV and DSV false-positive trends for 250 bp Illumina GA inserts and 40 kb fosmids (Table 2) for selected values of physical coverage (ρ = N λ/G).

Mentions: Thus far, concerns have predominantly focused on the rate of false-positive SV declarations. The general methodology has been one of assuming symmetric behavior of ISV and DSV and subsequently employing elementary Gaussian thresholds, usually ± 3 σ, to control false-positive errors [6,9-11,15]. For example, Tuzun et al. [6] aimed to identify SV of size δ ≥ 8 kb using fosmids. Fig. 2 revisits this aspect of the problem with respect to heterozygous SV for the edge cases of Illumina Genome Analyzer (GA) short inserts and large-insert fosmids (Table 2). Here, we demonstrate that false-positive behavior is more complex than what simple Gaussian thresholds are able to capture.


Statistical aspects of discerning indel-type structural variation via DNA sequence alignment.

Wendl MC, Wilson RK - BMC Genomics (2009)

Heterozygous ISV and DSV false-positive trends for 250 bp Illumina GA inserts and 40 kb fosmids (Table 2) for selected values of physical coverage (ρ = N λ/G).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2748092&req=5

Figure 2: Heterozygous ISV and DSV false-positive trends for 250 bp Illumina GA inserts and 40 kb fosmids (Table 2) for selected values of physical coverage (ρ = N λ/G).
Mentions: Thus far, concerns have predominantly focused on the rate of false-positive SV declarations. The general methodology has been one of assuming symmetric behavior of ISV and DSV and subsequently employing elementary Gaussian thresholds, usually ± 3 σ, to control false-positive errors [6,9-11,15]. For example, Tuzun et al. [6] aimed to identify SV of size δ ≥ 8 kb using fosmids. Fig. 2 revisits this aspect of the problem with respect to heterozygous SV for the edge cases of Illumina Genome Analyzer (GA) short inserts and large-insert fosmids (Table 2). Here, we demonstrate that false-positive behavior is more complex than what simple Gaussian thresholds are able to capture.

Bottom Line: Conversely, no significant improvement would be realized in lowering fosmid variances beyond current levels.Detection power is examined under a straightforward alternative hypothesis and found to be generally acceptable.At 1% risk, many designs will leave a significant gap in the 100 to 200 bp neighborhood, requiring unacceptably high redundancies to compensate.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Genome Center and Department of Genetics, Washington University, St Louis, MO 63108, USA. mwendl@wustl.edu

ABSTRACT

Background: Structural variations in the form of DNA insertions and deletions are an important aspect of human genetics and especially relevant to medical disorders. Investigations have shown that such events can be detected via tell-tale discrepancies in the aligned lengths of paired-end DNA sequencing reads. Quantitative aspects underlying this method remain poorly understood, despite its importance and conceptual simplicity. We report the statistical theory characterizing the length-discrepancy scheme for Gaussian libraries, including coverage-related effects that preceding models are unable to account for.

Results: Deletion and insertion statistics both depend heavily on physical coverage, but otherwise differ dramatically, refuting a commonly held doctrine of symmetry. Specifically, coverage restrictions render insertions much more difficult to capture. Increased read length has the counterintuitive effect of worsening insertion detection characteristics of short inserts. Variance in library insert length is also a critical factor here and should be minimized to the greatest degree possible. Conversely, no significant improvement would be realized in lowering fosmid variances beyond current levels. Detection power is examined under a straightforward alternative hypothesis and found to be generally acceptable. We also consider the proposition of characterizing variation over the entire spectrum of variant sizes under constant risk of false-positive errors. At 1% risk, many designs will leave a significant gap in the 100 to 200 bp neighborhood, requiring unacceptably high redundancies to compensate. We show that a few modifications largely close this gap and we give a few examples of feasible spectrum-covering designs.

Conclusion: The theory resolves several outstanding issues and furnishes a general methodology for designing future projects from the standpoint of a spectrum-wide constant risk.

Show MeSH