Derivation of DNA copy number concentration in the final reaction chamber with and without STA.

<p>Where <i>A</i> =  stock DNA concentration (ng/µL); <i>l</i> =  length in bp (human and whale genomes ∼3×10⁹ bp); V₁ =  DNA sample volume for STA (1.25 µL); V₂ =  STA mixture volume (5 µL); n =  Total number of PCR cycles; V₃ =  Pooled mixture volume, which is derived by multiplying V₂ and the number of SNP-GT assays (V₃ = V₂×SNP-GT assays); D =  Dilution factor (5- or 20- fold); V₄ =  DNA sample volume for genotyping (2.1 µL); V₅ =  GT sample solution volume (5 µL) and V₆ =  Reaction chamber volume (6.75 nL)<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039181#pone.0039181-Wang1" target="_blank">[9]</a>.</p><p><i>E_SX</i> was calculated assuming 100% PCR efficiency.</p>†<p>Use equations 1, 5–6 when estimating copies/reaction chamber without STA.</p><p>Use equations 1–6 when estimating copies/reaction chamber with STA in simplex.</p><p>Use equations 1–3, 4^♦ and 5–6 when estimating copies/reaction chamber with STA in Multiplex.</p>*<p>The Avogadro number (6.02214179×10²³) was taken from Mohr et al<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039181#pone.0039181-Mohr1" target="_blank">[20]</a> (CODATA-2006).</p><p>•Average molecular weight of DNA base pair used was 615.8771<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039181#pone.0039181-Doleel1" target="_blank">[21]</a>.</p><p>NA – refers to Not Applicable.</p

Effect of starting copy number on genotype call rate with and without STA.

<p>[A] and <b>[B]</b> Call map view and scatter plots of three human genomic DNA samples showing clustering (<b>pp</b>-‘<b>red</b>’, <b>qq</b>-‘<b>green</b>’ and <b>pq</b> ‘<b>blue</b>’) for a single SNP with and without STA. Black and Grey colors correspond to No Calls. The reaction chambers contained different copies ranging, on average, from approximately 97 to 1 copies(y) without STA and 2.0×10⁴ to 1.6×10² copies with STA. SNP-GT assay (rs513349) was loaded into sixteen separate assay inlets evenly spaced across the 48.48GT array. The remaining inlets were loaded with a NPC as stated in the Methods section.</p

Genotyping analysis workflow with and without STA.

<p><b>[A]</b> Steps 1–5 (denoted in red arrows) correspond to TaqMan^® SNP-GT protocol without STA or following simplex or multiplex STA. <b>[B]</b> Steps 1, 6–9 corresponds to STA reaction setup in simplex and multiplex conditions. Post STA, the amplified products are pooled (simplex STA), or further diluted 5 or 20 fold (multiplex STA) prior to performing TaqMan^® SNP-GT setup using steps 2–5.</p

Estimated DNA copy number in the reaction chamber with (simplex or multiplex) and without STA using whale genomic DNA.

<p> <i>The DNA copy number in the reaction chamber (E_RC) was estimated using equations (1–6) derived in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039181#pone-0039181-t001" target="_blank">Table 1</a>.</i></p>*<p> <i>The copies/reaction chamber post-simplex and multiplex STA PCR is an estimate obtained when using 15 SNP-GT assays with a 5 –fold dilution post STA.</i></p

Effect of DNA copy number on reliability of genotype call data for a heterozygous human genomic DNA sample, NA17316.

<p> <i>Call rate and call accuracy (%) at different number of copies per reaction chamber and for pq calls were determined from 144 data points.</i></p><p> <i>⁽¹⁾% Call rate [All Calls]  = 100*[(Total number of calls) / (Total number of calls + No Calls)].</i></p><p> <i>⁽²⁾% Call rate [pq Calls]  =  100*[(Correct Calls) / (Total number of calls + No Calls)].</i></p><p> <i>⁽³⁾% Call accuracy [pq Calls]  = 100*[(Correct Calls) / (Total number of calls)].</i></p

Summary genotype calls obtained for representative whale DNA samples.

<p>Genotype calls obtained for representative whale DNA samples extracted using CTAB or Maxwell^® tissue extraction kit and following simplex or multiplex STA using either 15 [A] or 45 SNP-GT assays [B]. The genotype call (<b>pp</b>, <b>qq</b> and <b>pq</b>) for each reaction are denoted in ‘<b>red</b>’, ‘<b>green</b>’ and ‘<b>blue</b>’, respectively. ‘+’ refers to samples extracted using CTAB method; '*' refers to each sample extracted using both CTAB and Maxwell^® tissue extraction kit; ‘♦’ refers to concordance with true genotype determined at AAD using an independent method. Note: Regardless of the approach used, genotypes for representative samples using either 15 or 45 SNP-GT assays were the same, as indicated by the same color. Samples EG09-004, EVH09-53, WA07-006 and WA07-003, extracted using CTAB or Maxwell^® tissue extraction kit were genotyped using 15 SNP-GT assays with and without STA and showed a 100% call rate and concordance (data not shown).</p

Scatter plots showing genotype call clusters for 46 whale samples using one assay (Exonic MALL).

<p>The groups (<b>pp</b>-‘<b>red</b>’, <b>qq</b>-‘<b>green</b>’ and <b>pq</b> ‘<b>blue</b>’) are denoted in circles.</p

Samples analysed using the SNP-GT nanofluidic system.

<p>Samples analysed using the SNP-GT nanofluidic system.</p

Effect of reaction DNA copy number on genotype call accuracy for a heterozygous (pq) sample.

<p>Call map view <b>[A]</b> and scatter plots <b>[B]</b> of the genotype calls from reaction chambers containing predicted 38, 18, 7, 4 and 1 copies(y). The genotype call (<b>pp</b>, <b>qq</b> and <b>pq</b>) for each reaction is denoted in ‘<b>red</b>’, ‘<b>green</b>’ and ‘<b>blue</b>’, respectively. No Call and NPC are denoted in ‘grey’ and NTCs in ‘black’. SNP-GT assay (rs513349) was loaded into sixteen separate assay inlets evenly spaced across the 48.48GT array. The remaining inlets were loaded with a NPC as stated in the Methods section.</p

Evaluation of a Droplet Digital Polymerase Chain Reaction Format for DNA Copy Number Quantification

Droplet digital polymerase chain reaction (ddPCR) is a new technology that was recently commercialized to enable the precise quantification of target nucleic acids in a sample. ddPCR measures absolute quantities by counting nucleic acid molecules encapsulated in discrete, volumetrically defined, water-in-oil droplet partitions. This novel ddPCR format offers a simple workflow capable of generating highly stable partitioning of DNA molecules. In this study, we assessed key performance parameters of the ddPCR system. A linear ddPCR response to DNA concentration was obtained from 0.16% through to 99.6% saturation in a 20,000 droplet assay corresponding to more than 4 orders of magnitude of target DNA copy number per ddPCR. Analysis of simplex and duplex assays targeting two distinct loci in the Lambda DNA genome using the ddPCR platform agreed, within their expanded uncertainties, with values obtained using a lower density microfluidic chamber based digital PCR (cdPCR). A relative expanded uncertainty under 5% was achieved for copy number concentration using ddPCR. This level of uncertainty is much lower than values typically observed for quantification of specific DNA target sequences using currently commercially available real-time and digital cdPCR technologies