Illumina DNA test panel-based genotyping of whole genome amplified-DNA extracted from hair samples: performance and agreement with genotyping results from genomic DNA from buccal cells

Agalliu, Ilir; Schweitzer, Peter A.; Leanza, Suzanne; Burk, Robert D.; Rohan, Thomas E.

doi:10.1515/cclm.2009.106

Cited by 4 publications

(3 citation statements)

References 22 publications

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“… 2 , 3 , 11 , 30 , 31 It was interesting to find that ATS were comparable to blood and other tissue samples that, with the exception of FFPE, are historically considered ideal specimens. The ease of collection, storage, and lower cost of sample shipment and extraction make ATS a valuable resource to stand alone or complement other specimens that may be limited in quality, 32 , 33 scope, 34 , 35 or yield 36 , 37 (see Supplemental Table S1 at http://jmd.amjpathol.org ). Depending on the research question, availability, or purpose, several different tissues may need to be analyzed in parallel to obtain an accurate genomic profile.…”

Section: Discussionmentioning

confidence: 99%

Comparative Analytical Utility of DNA Derived from Alternative Human Specimens for Molecular Autopsy and Diagnostics

Klassen

Rüden

Drabek

et al. 2012

The Journal of Molecular Diagnostics

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Genetic testing and research have increased the demand for high-quality DNA that has traditionally been obtained by venipuncture. However, venous blood collection may prove difficult in special populations and when large-scale specimen collection or exchange is prerequisite for international collaborative investigations. Guthrie/FTA card–based blood spots, buccal scrapes, and finger nail clippings are DNA-containing specimens that are uniquely accessible and thus attractive as alternative tissue sources (ATS). The literature details a variety of protocols for extraction of nucleic acids from a singular ATS type, but their utility has not been systematically analyzed in comparison with conventional sources such as venous blood. Additionally, the efficacy of each protocol is often equated with the overall nucleic acid yield but not with the analytical performance of the DNA during mutation detection. Together with a critical in-depth literature review of published extraction methods, we developed and evaluated an all-inclusive approach for serial, systematic, and direct comparison of DNA utility from multiple biological samples. Our results point to the often underappreciated value of these alternative tissue sources and highlight ways to maximize the ATS-derived DNA for optimal quantity, quality, and utility as a function of extraction method. Our comparative analysis clarifies the value of ATS in genomic analysis projects for population-based screening, diagnostics, molecular autopsy, medico-legal investigations, or multi-organ surveys of suspected mosaicisms.

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Section: Discussionmentioning

confidence: 99%

Comparative Analytical Utility of DNA Derived from Alternative Human Specimens for Molecular Autopsy and Diagnostics

Klassen

Rüden

Drabek

et al. 2012

The Journal of Molecular Diagnostics

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“…The Illumina platform (Illumina Inc., San Diego, CA, USA) has proven reliable and efficient for a number of high-throughput genotyping applications using DNA extracted from several sources, [3-9]. VeraCode and BeadArray technologies are used with the GoldenGate assay (Illumina) developed for simultaneous determination of between 96 and 384 (VeraCode) and 96 and 1,536 (BeadArray) variants.…”

Section: Introductionmentioning

confidence: 99%

Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation

et al. 2010

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BackgroundHigh-throughput custom designed genotyping arrays are a valuable resource for biologically focused research studies and increasingly for validation of variation predicted by next-generation sequencing (NGS) technologies. We investigate the Illumina GoldenGate chemistry using custom designed VeraCode and sentrix array matrix (SAM) assays for each of these applications, respectively. We highlight applications for interpretation of Illumina generated genotype cluster plots to maximise data inclusion and reduce genotyping errors.FindingsWe illustrate the dramatic effect of outliers in genotype calling and data interpretation, as well as suggest simple means to avoid genotyping errors. Furthermore we present this platform as a successful method for two-cluster rare or non-autosomal variant calling. The success of high-throughput technologies to accurately call rare variants will become an essential feature for future association studies. Finally, we highlight additional advantages of the Illumina GoldenGate chemistry in generating unusually segregated cluster plots that identify potential NGS generated sequencing error resulting from minimal coverage.ConclusionsWe demonstrate the importance of visually inspecting genotype cluster plots generated by the Illumina software and issue warnings regarding commonly accepted quality control parameters. In addition to suggesting applications to minimise data exclusion, we propose that the Illumina cluster plots may be helpful in identifying potential in-put sequence errors, particularly important for studies to validate NGS generated variation.

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“…Furthermore, buccal cell sample collection is minimally invasive, allowing study subjects to collect their sample from home and send it back via the mail, which can maximize participation when the study population is geographically dispersed. [1][2][3][4][5][6] However, inadequate DNA yield, [3][4][5][6] the presence of bacterial DNA, 7 and the need to possibly store samples for long periods prior to use may compromise the utility of buccal cell samples for GWAS. Re-sampling in aging cohorts to augment DNA concentrations may not be an option because of limited resources, loss to follow up, or death of cohort members.…”

Section: Introductionmentioning

confidence: 99%

Feasibility of High-Throughput Genome-Wide Genotyping using DNA from Stored Buccal Cell Samples

et al. 2010

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It is unclear if buccal cell samples contain sufficient human DNA with adequately sized fragments for high throughput genetic bioassays. Yet buccal cell sample collection is an attractive alternative to gathering blood samples for genetic epidemiologists engaged in large-scale genetic biomarker studies. We assessed the genotyping efficiency (GE) and genotyping concordance (GC) of buccal cell DNA samples compared to corresponding blood DNA samples, from 32 Nurses’ Health Study (NHS) participants using the Illumina Infinium 660W-Quad platform. We also assessed how GE and GC accuracy varied as a function of DNA concentration using serial dilutions of buccal DNA samples. Finally we determined the nature and genomic distribution of discordant genotypes in buccal DNA samples. The mean GE of undiluted buccal cell DNA samples was high (99.32%), as was the GC between the paired buccal and blood samples (99.29%). GC between the dilutions versus the undiluted buccal DNA was also very high (>97%), though both GE and GC notably declined at DNA concentrations less than 5 ng/μl. Most (>95%) genotype determinations in buccal cell samples were of the “missing call” variety (as opposed to the “alternative genotype call” variety) across the spectrum of buccal DNA concentrations studied. Finally, for buccal DNA concentration above 1.7 ng/ul, discordant genotyping calls did not cluster in any particular chromosome. Buccal cell-derived DNA represents a viable alternative to blood DNA for genotyping on a high-density platform.

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Illumina DNA test panel-based genotyping of whole genome amplified-DNA extracted from hair samples: performance and agreement with genotyping results from genomic DNA from buccal cells

Cited by 4 publications

References 22 publications

Comparative Analytical Utility of DNA Derived from Alternative Human Specimens for Molecular Autopsy and Diagnostics

Comparative Analytical Utility of DNA Derived from Alternative Human Specimens for Molecular Autopsy and Diagnostics

Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation

Feasibility of High-Throughput Genome-Wide Genotyping using DNA from Stored Buccal Cell Samples

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