Analysis of archived residual newborn screening blood spots after whole genome amplification.
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.
Baylor Health, Baylor Institute for Immunology Research, 3434 Live Oak Street, Dallas, TX, 75204, USA. brandi.cantarel@baylorhealth.edu.
Brandi L
BL
Cantarel
Department of Nutritional Sciences, Dell Pediatric Research Institute, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX, 78723, USA. yunping@austin.utexas.edu.
Yunping
Y
Lei
Genformatic, 6301 Highland Hills Drive, Austin, TX, 78731, USA. dbeeweaver@gmail.com.
Daniel
D
Weaver
Department of Nutritional Sciences, Dell Pediatric Research Institute, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX, 78723, USA. zhuhuiping@hotmail.com.|Present address: Asuragen Inc, 2150 Woodward Street #100, Austin, TX, 78744, USA. zhuhuiping@hotmail.com.
Huiping
H
Zhu
Department of Biology, Boston College, Boston, MA, 02467, USA. andrew.farrell@bc.edu.
Andrew
A
Farrell
Department of Biology, Boston College, Boston, MA, 02467, USA. graemebh@gmail.com.
Graeme
G
Benstead-Hume
Justin
J
Reese
Department of Nutritional Sciences, Dell Pediatric Research Institute, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX, 78723, USA. rfinnell@austin.utexas.edu.
Richard H
RH
Finnell
D019295:Computational Biology / Q000379:methods; D059788:Dried Blood Spot Testing / Q000379:methods; D059472:Exome; D015894:Genome, Human; D006801:Humans; D007231:Infant, Newborn; D015997:Neonatal Screening / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*