Analysis of archived residual newborn screening blood spots after whole genome amplification

Brandi L. Cantarel, Yunping Lei, Daniel Weaver, Huiping Zhu, Andrew Farrell, Graeme Benstead-Hume, Justin Reese, Richard H. Finnell

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Background: Deidentified newborn screening bloodspot samples (NBS) represent a valuable potential resource for genomic research if impediments to whole exome sequencing of NBS deoxyribonucleic acid (DNA), including the small amount of genomic DNA in NBS material, can be overcome. For instance, genomic analysis of NBS could be used to define allele frequencies of disease-associated variants in local populations, or to conduct prospective or retrospective studies relating genomic variation to disease emergence in pediatric populations over time. In this study, we compared the recovery of variant calls from exome sequences of amplified NBS genomic DNA to variant calls from exome sequencing of non-amplified NBS DNA from the same individuals. Results: Using a standard alignment-based Genome Analysis Toolkit (GATK), we find 62,000-76,000 additional variants in amplified samples. After application of a unique kmer enumeration and variant detection method (RUFUS), only 38,000-47,000 additional variants are observed in amplified gDNA. This result suggests that roughly half of the amplification-introduced variants identified using GATK may be the result of mapping errors and read misalignment. Conclusions: Our results show that it is possible to obtain informative, high-quality data from exome analysis of whole genome amplified NBS with the important caveat that different data generation and analysis methods can affect variant detection accuracy, and the concordance of variant calls in whole-genome amplified and non-amplified exomes.

Original languageEnglish (US)
Article number602
JournalBMC Genomics
Volume16
Issue number1
DOIs
StatePublished - Aug 13 2015

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Exome
Genome
DNA
Gene Frequency
Population
Retrospective Studies
Prospective Studies
Pediatrics
Research

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Cantarel, B. L., Lei, Y., Weaver, D., Zhu, H., Farrell, A., Benstead-Hume, G., ... Finnell, R. H. (2015). Analysis of archived residual newborn screening blood spots after whole genome amplification. BMC Genomics, 16(1), [602]. https://doi.org/10.1186/s12864-015-1747-2

Analysis of archived residual newborn screening blood spots after whole genome amplification. / Cantarel, Brandi L.; Lei, Yunping; Weaver, Daniel; Zhu, Huiping; Farrell, Andrew; Benstead-Hume, Graeme; Reese, Justin; Finnell, Richard H.

In: BMC Genomics, Vol. 16, No. 1, 602, 13.08.2015.

Research output: Contribution to journalArticle

Cantarel, BL, Lei, Y, Weaver, D, Zhu, H, Farrell, A, Benstead-Hume, G, Reese, J & Finnell, RH 2015, 'Analysis of archived residual newborn screening blood spots after whole genome amplification', BMC Genomics, vol. 16, no. 1, 602. https://doi.org/10.1186/s12864-015-1747-2
Cantarel, Brandi L. ; Lei, Yunping ; Weaver, Daniel ; Zhu, Huiping ; Farrell, Andrew ; Benstead-Hume, Graeme ; Reese, Justin ; Finnell, Richard H. / Analysis of archived residual newborn screening blood spots after whole genome amplification. In: BMC Genomics. 2015 ; Vol. 16, No. 1.
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