Analysis of Archived Residual Newborn Screening Blood Spots After Whole Genome Amplification

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dc.contributor.utaustinauthorZhu, Huipingen_US
dc.contributor.utaustinauthorFinnell, Richard H.en_US
dc.creatorCantarel, Brandi L.en_US
dc.creatorLei, Yunpingen_US
dc.creatorWeaver, Danielen_US
dc.creatorZhu, Huipingen_US
dc.creatorFarrell, Andrewen_US
dc.creatorBenstead-Hume, Graemeen_US
dc.creatorReese, Justinen_US
dc.creatorFinnell, Richard H.en_US
dc.date.accessioned2016-10-28T19:53:24Z
dc.date.available2016-10-28T19:53:24Z
dc.date.issued2015-08en_US
dc.description.abstractDeidentified 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.en_US
dc.description.departmentNutritional Sciencesen_US
dc.description.sponsorshipNational Institute of Health P01HD067244, NS076465, R01ES021006en_US
dc.identifierdoi:10.15781/T2K93188F
dc.identifier.citationCantarel, Brandi L., Yunping Lei, Daniel Weaver, Huiping Zhu, Andrew Farrell, Graeme Benstead-Hume, Justin Reese, and Richard H. Finnell. "Analysis of archived residual newborn screening blood spots after whole genome amplification." BMC genomics, Vol. 16, No. 1 (Aug., 2015): 602.en_US
dc.identifier.doi10.1186/s12864-015-1747-2en_US
dc.identifier.issn1471-2164en_US
dc.identifier.urihttp://hdl.handle.net/2152/43342
dc.language.isoEnglishen_US
dc.relation.ispartofen_US
dc.relation.ispartofserialBMC Genomicsen_US
dc.rightsAdministrative deposit of works to Texas ScholarWorks: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access or the publisher allows a PDF version of the article to be freely posted online. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en_US
dc.rights.restrictionOpenen_US
dc.subjectsamplesen_US
dc.subjectbiotechnology & applied microbiologyen_US
dc.subjectgenetics & heredityen_US
dc.titleAnalysis of Archived Residual Newborn Screening Blood Spots After Whole Genome Amplificationen_US
dc.typeArticleen_US

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