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Table 2.

WgaDNA concentrations and genotyping outcomes

WGA sample nameDNA quantification method
Illumina quality control metrics
Quantitative PCR Alu Yd6 (ng/μL)UV spectrophotometry (ng/μL)Fluorescence λ curve (ng/μL)Fluorescence calf thymus curve (ng/μL)WGA sample call frequency*Sample pair call frequency†Genotype concordance‡ (%)
High quality, >99% genotyping concordance        
    36-B 68.58 90.0 16.1 33.2 0.9844 0.9609 100.00 
    32-B 42.18 73.6 25.2 50.6 0.9870 0.9531 100.00 
    21-B 61.49 83.7 44.2 97.0 0.9766 0.9427 99.86 
    30-B 4.14 75.6 45.3 89.6 0.9844 0.9531 99.73 
    2-W 107.94 101.5 26.4 50.0 0.9818 0.9766 99.60 
    12-W 88.92 96.7 29.9 61.3 0.9792 0.9740 99.60 
    39-W 81.65 91.6 36.5 78.0 0.9792 0.9714 99.60 
    1-W 76.01 94.0 41.3 69.9 0.9792 0.9714 99.60 
    45-W 50.16 72.5 35.4 79.2 0.9792 0.9766 99.60 
    23-W 43.75 88.3 52.5 88.8 0.9792 0.9740 99.60 
    6-B 25.64 98.1 20.1 40.5 0.9818 0.9792 99.60 
    17-B 48.84 88.4 44.1 82.4 0.9844 0.9479 99.59 
    43-B 15.16 65.2 34.9 53.4 0.9818 0.9635 99.59 
    37-W 111.62 108.6 21.5 47.7 0.9792 0.9740 99.47 
    34-W 101.34 100.0 27.4 56.2 0.9818 0.9740 99.47 
    4-W 91.47 97.5 24.6 48.8 0.9844 0.9766 99.47 
    25-W 89.21 83.5 24.6 73.1 0.9818 0.9766 99.47 
    8-W 80.86 86.0 36.5 63.6 0.9792 0.9740 99.47 
    32-W 65.60 79.4 32.0 79.4 0.9766 0.9740 99.47 
    19-B 41.20 74.1 13.6 39.1 0.9870 0.9844 99.47 
    46-B 5.09 61.0 43.0 71.8 0.9792 0.9740 99.47 
    3-W 106.57 101.4 29.8 54.7 0.9792 0.9714 99.46 
    13-W 85.95 106.6 33.2 67.3 0.9766 0.9714 99.46 
    10-W 61.71 89.0 31.9 59.5 0.9766 0.9714 99.46 
    43-W 93.13 90.4 26.7 54.6 0.9818 0.9792 99.34 
    36-W 118.32 113.1 22.7 52.6 0.9766 0.9740 99.33 
    17-W 101.36 112.7 27.0 54.9 0.9844 0.9688 99.33 
    30-W 99.23 106.2 27.7 69.5 0.9792 0.9766 99.33 
    41-W 93.55 87.0 30.0 52.3 0.9792 0.9766 99.33 
    11-W 90.95 103.9 29.7 62.0 0.9818 0.9766 99.33 
    5-W 65.93 91.9 28.1 63.3 0.9792 0.9740 99.33 
    7-W 60.98 88.9 35.8 73.9 0.9792 0.9714 99.33 
    40-B 9.09 70.0 21.6 34.8 0.9792 0.9766 99.33 
    21-W 94.86 103.5 22.1 48.9 0.9792 0.9740 99.20 
    26-W 82.11 83.7 30.6 77.7 0.9870 0.9818 99.20 
    9-W 75.63 93.1 47.9 84.5 0.9740 0.9714 99.20 
    20-W 82.23 93.0 40.6 74.6 0.9740 0.9688 99.19 
    37-B 8.27 77.1 53.0 68.4 0.9844 0.9583 99.18 
    14-W 59.12 90.2 35.7 68.3 0.9792 0.9766 98.93 
    Average 68.97 90.0 32.0 63.5 0.9805 0.9710 99.46 
    SD 31.78 12.8 9.5 15.6 0.0033 0.0090 0.22 
    Range 4.14-118.32 61.0-113.1 13.6-53.0 33.2-97.0 0.9740-0.9870 0.9427-0.9844 98.93-100.00 
Moderate quality, >90-99% concordance        
    29-B 1.25 69.0 40.2 87.6 0.9818 0.9792 98.27 
    45-B 2.19 44.0 35.9 86.4 0.9635 0.9323 97.77 
    15-B 0.29 58.6 46.6 83.2 0.9740 0.9688 97.31 
    42-B 0.75 70.4 44.3 83.2 0.9792 0.9766 97.07 
    18-B 0.65 66.5 54.0 154.8 0.9870 0.9844 96.83 
    33-B 1.67 64.7 44.7 99.3 0.9740 0.9714 96.65 
    31-B 1.29 50.2 46.6 113.0 0.9766 0.9714 96.11 
    Average 1.15 60.5 44.6 101.1 0.9766 0.9692 97.14 
    SD 0.65 10.0 5.7 26.0 0.0074 0.0171 0.72 
    Range 0.29-2.19 44.0-70.4 35.9-54.0 83.2-154.8 0.9635-0.9870 0.9323-0.9844 96.11-98.27 
Poor quality, <90% concordance        
    27-B§ 0.01 53.1 40.6 84.2 0.8385 0.8333 76.09 
    16-B§ 0.24 54.3 50.6 86.0 0.8724 0.8698 75.15 
    24-B§ 0.27 62.1 52.6 139.0 0.8932 0.8828 74.04 
    44-B§ 0.19 61.1 50.1 130.8 0.8542 0.8490 71.01 
    38-B§ 0.04 65.7 42.0 92.3 0.8333 0.8281 68.08 
    35-B§ 0.08 59.8 47.3 141.4 0.7917 0.7865 67.72 
    28-B§ 0.02 62.3 47.2 97.2 0.8568 0.8516 67.28 
    22-B§ 0.26 57.7 48.6 102.3 0.8021 0.7969 65.03 
    Average 0.14 59.5 47.4 109.2 0.8428 0.8373 70.55 
    SD 0.11 4.3 4.2 24.0 0.0341 0.0333 4.13 
    Range 0.01-0.27 53.1-65.7 40.6-52.6 84.2-141.4 0.7917-0.8932 0.7865-0.8828 65.03-76.09 
WGA sample nameDNA quantification method
Illumina quality control metrics
Quantitative PCR Alu Yd6 (ng/μL)UV spectrophotometry (ng/μL)Fluorescence λ curve (ng/μL)Fluorescence calf thymus curve (ng/μL)WGA sample call frequency*Sample pair call frequency†Genotype concordance‡ (%)
High quality, >99% genotyping concordance        
    36-B 68.58 90.0 16.1 33.2 0.9844 0.9609 100.00 
    32-B 42.18 73.6 25.2 50.6 0.9870 0.9531 100.00 
    21-B 61.49 83.7 44.2 97.0 0.9766 0.9427 99.86 
    30-B 4.14 75.6 45.3 89.6 0.9844 0.9531 99.73 
    2-W 107.94 101.5 26.4 50.0 0.9818 0.9766 99.60 
    12-W 88.92 96.7 29.9 61.3 0.9792 0.9740 99.60 
    39-W 81.65 91.6 36.5 78.0 0.9792 0.9714 99.60 
    1-W 76.01 94.0 41.3 69.9 0.9792 0.9714 99.60 
    45-W 50.16 72.5 35.4 79.2 0.9792 0.9766 99.60 
    23-W 43.75 88.3 52.5 88.8 0.9792 0.9740 99.60 
    6-B 25.64 98.1 20.1 40.5 0.9818 0.9792 99.60 
    17-B 48.84 88.4 44.1 82.4 0.9844 0.9479 99.59 
    43-B 15.16 65.2 34.9 53.4 0.9818 0.9635 99.59 
    37-W 111.62 108.6 21.5 47.7 0.9792 0.9740 99.47 
    34-W 101.34 100.0 27.4 56.2 0.9818 0.9740 99.47 
    4-W 91.47 97.5 24.6 48.8 0.9844 0.9766 99.47 
    25-W 89.21 83.5 24.6 73.1 0.9818 0.9766 99.47 
    8-W 80.86 86.0 36.5 63.6 0.9792 0.9740 99.47 
    32-W 65.60 79.4 32.0 79.4 0.9766 0.9740 99.47 
    19-B 41.20 74.1 13.6 39.1 0.9870 0.9844 99.47 
    46-B 5.09 61.0 43.0 71.8 0.9792 0.9740 99.47 
    3-W 106.57 101.4 29.8 54.7 0.9792 0.9714 99.46 
    13-W 85.95 106.6 33.2 67.3 0.9766 0.9714 99.46 
    10-W 61.71 89.0 31.9 59.5 0.9766 0.9714 99.46 
    43-W 93.13 90.4 26.7 54.6 0.9818 0.9792 99.34 
    36-W 118.32 113.1 22.7 52.6 0.9766 0.9740 99.33 
    17-W 101.36 112.7 27.0 54.9 0.9844 0.9688 99.33 
    30-W 99.23 106.2 27.7 69.5 0.9792 0.9766 99.33 
    41-W 93.55 87.0 30.0 52.3 0.9792 0.9766 99.33 
    11-W 90.95 103.9 29.7 62.0 0.9818 0.9766 99.33 
    5-W 65.93 91.9 28.1 63.3 0.9792 0.9740 99.33 
    7-W 60.98 88.9 35.8 73.9 0.9792 0.9714 99.33 
    40-B 9.09 70.0 21.6 34.8 0.9792 0.9766 99.33 
    21-W 94.86 103.5 22.1 48.9 0.9792 0.9740 99.20 
    26-W 82.11 83.7 30.6 77.7 0.9870 0.9818 99.20 
    9-W 75.63 93.1 47.9 84.5 0.9740 0.9714 99.20 
    20-W 82.23 93.0 40.6 74.6 0.9740 0.9688 99.19 
    37-B 8.27 77.1 53.0 68.4 0.9844 0.9583 99.18 
    14-W 59.12 90.2 35.7 68.3 0.9792 0.9766 98.93 
    Average 68.97 90.0 32.0 63.5 0.9805 0.9710 99.46 
    SD 31.78 12.8 9.5 15.6 0.0033 0.0090 0.22 
    Range 4.14-118.32 61.0-113.1 13.6-53.0 33.2-97.0 0.9740-0.9870 0.9427-0.9844 98.93-100.00 
Moderate quality, >90-99% concordance        
    29-B 1.25 69.0 40.2 87.6 0.9818 0.9792 98.27 
    45-B 2.19 44.0 35.9 86.4 0.9635 0.9323 97.77 
    15-B 0.29 58.6 46.6 83.2 0.9740 0.9688 97.31 
    42-B 0.75 70.4 44.3 83.2 0.9792 0.9766 97.07 
    18-B 0.65 66.5 54.0 154.8 0.9870 0.9844 96.83 
    33-B 1.67 64.7 44.7 99.3 0.9740 0.9714 96.65 
    31-B 1.29 50.2 46.6 113.0 0.9766 0.9714 96.11 
    Average 1.15 60.5 44.6 101.1 0.9766 0.9692 97.14 
    SD 0.65 10.0 5.7 26.0 0.0074 0.0171 0.72 
    Range 0.29-2.19 44.0-70.4 35.9-54.0 83.2-154.8 0.9635-0.9870 0.9323-0.9844 96.11-98.27 
Poor quality, <90% concordance        
    27-B§ 0.01 53.1 40.6 84.2 0.8385 0.8333 76.09 
    16-B§ 0.24 54.3 50.6 86.0 0.8724 0.8698 75.15 
    24-B§ 0.27 62.1 52.6 139.0 0.8932 0.8828 74.04 
    44-B§ 0.19 61.1 50.1 130.8 0.8542 0.8490 71.01 
    38-B§ 0.04 65.7 42.0 92.3 0.8333 0.8281 68.08 
    35-B§ 0.08 59.8 47.3 141.4 0.7917 0.7865 67.72 
    28-B§ 0.02 62.3 47.2 97.2 0.8568 0.8516 67.28 
    22-B§ 0.26 57.7 48.6 102.3 0.8021 0.7969 65.03 
    Average 0.14 59.5 47.4 109.2 0.8428 0.8373 70.55 
    SD 0.11 4.3 4.2 24.0 0.0341 0.0333 4.13 
    Range 0.01-0.27 53.1-65.7 40.6-52.6 84.2-141.4 0.7917-0.8932 0.7865-0.8828 65.03-76.09 

Abbreviations: B, buccal swab wgaDNA; W, whole blood wgaDNA.

*

Genotypes with GenCall score <0.25 were not included in the analysis (GenCall threshold as defined in Illumina BeadStation 500G System Manual Rev. B, p. 4-8: “…a value between 0 and 1 that indicates the confidence in that call. A higher score indicates a higher confidence in the call. The score is a function of the quality of the genotype clusters… and the position of that specific DNA sample relative to its corresponding cluster”).

†

Genotype pairs were evaluated where both genotypes had a GenCall score >0.25.

‡

(Total number of matching genotypes / total number of genotype pairs passing quality control) × 100.

§

Failed sample [samples with a sample call frequency >0.969 were designated as passed, those with <0.969 (less than an unamplified blank) as failed].

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