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Variant discovery in targeted resequencing using whole genome amplified DNA.

Indap AR, Cole R, Runge CL, Marth GT, Olivier M - BMC Genomics (2013)

Bottom Line: Next generation sequencing and advances in genomic enrichment technologies have enabled the discovery of the full spectrum of variants from common to rare alleles in the human population.The application of such technologies can be limited by the amount of DNA available.Whole genome amplification (WGA) can overcome such limitations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Boston College, Chestnut Hill, MA, USA. indapa@gmail.com

ABSTRACT

Background: Next generation sequencing and advances in genomic enrichment technologies have enabled the discovery of the full spectrum of variants from common to rare alleles in the human population. The application of such technologies can be limited by the amount of DNA available. Whole genome amplification (WGA) can overcome such limitations. Here we investigate applicability of using WGA by comparing SNP and INDEL variant calls from a single genomic/WGA sample pair from two capture separate experiments: a 50 Mbp whole exome capture and a custom capture array of 4 Mbp region on chr12.

Results: Our results comparing variant calls derived from genomic and WGA DNA show that the majority of variant SNP and INDEL calls are common to both callsets, both at the site and genotype level and suggest that allele bias plays a minimal role when using WGA DNA in re-sequencing studies.

Conclusions: Although the results of this study are based on a limited sample size, they suggest that using WGA DNA allows the discovery of the vast majority of variants, and achieves high concordance metrics, when comparing to genomic DNA calls.

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Related in: MedlinePlus

Number of variants discovered in downsampled and subsetted WGA BAMs. Median number of SNPs and INDELs called from 100 bootstrap subsampled BAM files from whole-exome and chr12 capture experiments for WGA DNA samples. Plot also includes number of variants discovered in the WGA subsetted BAM that matched the starting read count of the genomic sample.
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Figure 3: Number of variants discovered in downsampled and subsetted WGA BAMs. Median number of SNPs and INDELs called from 100 bootstrap subsampled BAM files from whole-exome and chr12 capture experiments for WGA DNA samples. Plot also includes number of variants discovered in the WGA subsetted BAM that matched the starting read count of the genomic sample.

Mentions: Figure 3 shows the median number of variants discovered as a function of average target coverage for SNPs and INDELs, for each capture experiment. The randomly chosen subset of WGA reads to match the number of PF reads in the genomic sequencing experiment is shown as genomic.matched on the x-axis, and sorted in ascending order of target coverage. As expected, downsampling BAMs reduces the number of called variants, with the original WGA BAM having the largest number of called variants. The datapoint that most closely matches the target coverage of the non-WGA sample is 80x for the whole-exome plot. The median number of SNPs and INDELs found (29350 and 2174) closely match the numbers of variants found the in genomic derived variant calls listed in Table 1. The datapoint that most closely matches the target coverage non-WGA sample is 200x for the chr12 plot. The median number of SNPs and INDELs found (4615,483), again closely match what was found in the genomic derived calls listed in Table 1.


Variant discovery in targeted resequencing using whole genome amplified DNA.

Indap AR, Cole R, Runge CL, Marth GT, Olivier M - BMC Genomics (2013)

Number of variants discovered in downsampled and subsetted WGA BAMs. Median number of SNPs and INDELs called from 100 bootstrap subsampled BAM files from whole-exome and chr12 capture experiments for WGA DNA samples. Plot also includes number of variants discovered in the WGA subsetted BAM that matched the starting read count of the genomic sample.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3716764&req=5

Figure 3: Number of variants discovered in downsampled and subsetted WGA BAMs. Median number of SNPs and INDELs called from 100 bootstrap subsampled BAM files from whole-exome and chr12 capture experiments for WGA DNA samples. Plot also includes number of variants discovered in the WGA subsetted BAM that matched the starting read count of the genomic sample.
Mentions: Figure 3 shows the median number of variants discovered as a function of average target coverage for SNPs and INDELs, for each capture experiment. The randomly chosen subset of WGA reads to match the number of PF reads in the genomic sequencing experiment is shown as genomic.matched on the x-axis, and sorted in ascending order of target coverage. As expected, downsampling BAMs reduces the number of called variants, with the original WGA BAM having the largest number of called variants. The datapoint that most closely matches the target coverage of the non-WGA sample is 80x for the whole-exome plot. The median number of SNPs and INDELs found (29350 and 2174) closely match the numbers of variants found the in genomic derived variant calls listed in Table 1. The datapoint that most closely matches the target coverage non-WGA sample is 200x for the chr12 plot. The median number of SNPs and INDELs found (4615,483), again closely match what was found in the genomic derived calls listed in Table 1.

Bottom Line: Next generation sequencing and advances in genomic enrichment technologies have enabled the discovery of the full spectrum of variants from common to rare alleles in the human population.The application of such technologies can be limited by the amount of DNA available.Whole genome amplification (WGA) can overcome such limitations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Boston College, Chestnut Hill, MA, USA. indapa@gmail.com

ABSTRACT

Background: Next generation sequencing and advances in genomic enrichment technologies have enabled the discovery of the full spectrum of variants from common to rare alleles in the human population. The application of such technologies can be limited by the amount of DNA available. Whole genome amplification (WGA) can overcome such limitations. Here we investigate applicability of using WGA by comparing SNP and INDEL variant calls from a single genomic/WGA sample pair from two capture separate experiments: a 50 Mbp whole exome capture and a custom capture array of 4 Mbp region on chr12.

Results: Our results comparing variant calls derived from genomic and WGA DNA show that the majority of variant SNP and INDEL calls are common to both callsets, both at the site and genotype level and suggest that allele bias plays a minimal role when using WGA DNA in re-sequencing studies.

Conclusions: Although the results of this study are based on a limited sample size, they suggest that using WGA DNA allows the discovery of the vast majority of variants, and achieves high concordance metrics, when comparing to genomic DNA calls.

Show MeSH
Related in: MedlinePlus