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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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Spectral curves for heterozygous ISV at a threshold of α = 1% for both conventional insert types (Table 2) and hypothetical Illumina GA inserts having one-third lower (improved) COV values. Bold lines represent two feasible designs that leave no spectral gaps at α = 1% using the improved GA libraries.
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Figure 6: Spectral curves for heterozygous ISV at a threshold of α = 1% for both conventional insert types (Table 2) and hypothetical Illumina GA inserts having one-third lower (improved) COV values. Bold lines represent two feasible designs that leave no spectral gaps at α = 1% using the improved GA libraries.

Mentions: Fig. 6 addresses the design issue from the standpoint of the "spectral chart", which is readily plotted from the theory. In particular, the solid curves represent the loci of points at which the desired α, in this case 1% [6,10,11,15], is realized for the conventional inserts listed in Table 2. (We omit the pyrosequencing-454 insert, whose relatively large COV renders it less suitable for SV applications compared to the comparable Illumina GA library [8].) The dashed curves denote improved performance of hypothetical Illumina GA libraries whose COVs are one-third lower than conventional values.


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

Wendl MC, Wilson RK - BMC Genomics (2009)

Spectral curves for heterozygous ISV at a threshold of α = 1% for both conventional insert types (Table 2) and hypothetical Illumina GA inserts having one-third lower (improved) COV values. Bold lines represent two feasible designs that leave no spectral gaps at α = 1% using the improved GA libraries.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Spectral curves for heterozygous ISV at a threshold of α = 1% for both conventional insert types (Table 2) and hypothetical Illumina GA inserts having one-third lower (improved) COV values. Bold lines represent two feasible designs that leave no spectral gaps at α = 1% using the improved GA libraries.
Mentions: Fig. 6 addresses the design issue from the standpoint of the "spectral chart", which is readily plotted from the theory. In particular, the solid curves represent the loci of points at which the desired α, in this case 1% [6,10,11,15], is realized for the conventional inserts listed in Table 2. (We omit the pyrosequencing-454 insert, whose relatively large COV renders it less suitable for SV applications compared to the comparable Illumina GA library [8].) The dashed curves denote improved performance of hypothetical Illumina GA libraries whose COVs are one-third lower than conventional values.

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