Skip to main content

Table 4 Comparison between allele frequencies generated using Sequenom® MassARRAY and Illumina GAIIx technologies.

From: Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

EntrezGene ID Chr. SNP name1 Position Allele sub.2 Allele frequency in low CIV pool3 P value4 Allele frequency in high CIV pool3 P value4 Reference5
      Actual NGS   Actual NGS   
   S555G 33897071 T > C 0.19 0.15 1.00 0.12 0.10 1.00 AF140284
   H545 33897099 A > G 0.34 0.28 0.96 0.15 0.18 1.00 AF140284
   A536T 33897128 C > T 0.13 0.15 1.00 0.02 0.00 1.00 AF140284
   N528T 33897151 T > G 0.21 0.22 1.00 0.12 0.10 1.00 AM161140
   GHR76 33897252 A > G 0.13 0.14 1.00 0.02 0.00 1.00 n/a
   F279Y 33915503 A > T 0.00 0.00 1.00 0.09 0.09 1.00 AM161140
   GHR19.1 33994639 G > T 0.62 0.65 1.00 0.47 0.29 0.23 rs109702942
   GHR18.2 33995251 G > C 0.07 0.09 1.00 0.00 0.00 1.00 n/a
   AF126288:g.149 34086084 C > T 0.69 0.73 1.00 0.31 0.29 1.00 AF126288
GHR 20 GHR9.1 34101240 C > T 0.05 0.00 0.96 0.37 0.33 1.00 rs110979028
   GHR3.3 34166627 A > G 0.08 0.12 1.00 0.43 0.39 1.00 n/a
   GHR3.2 34166731 A > G 0.09 0.13 1.00 0.43 0.31 0.96 n/a
   GHR3.1 34166898 T > C 0.09 0.00 0.23 0.42 0.33 0.96 n/a
   GHR2.6 34166944 C > T 0.09 0.00 0.22 0.42 0.38 1.00 rs109825954
   GHR2.5 34166970 A > G 0.09 0.00 0.23 0.42 0.36 1.00 n/a
   GHR2.4 34166982 A > C 0.09 0.00 0.22 0.43 0.33 0.96 n/a
   GHR2.3 34167025 C > T 0.09 0.00 0.23 0.42 0.37 1.00 n/a
   GHR2.2 34167126 G > A 0.09 0.09 1.00 0.43 0.35 1.00 n/a
   GHR2.1 34167240 C > T 0.09 0.00 0.13 0.44 0.52 1.00 n/a
   GH19 49657225 G > A 0.90 0.86 1.00 0.84 0.91 1.00 rs41923481
   GH18 49657293 G > A 0.92 0.82 1.00 0.92 0.90 1.00 rs196003433
   GH17 49657371 C > G 0.92 1.00 1.00 0.89 1.00 1.00 rs41923483
   2291 49660125 T > G 0.08 0.00 0.13 0.12 0.08 1.00 n/a
   2141 49660275 G > C 0.33 0.36 1.00 0.09 0.11 1.00 rs41923484
   GH6 49660469 A > C 0.08 0.00 0.96 0.12 0.12 1.00 rs196003424
   GH38 49693278 G > A 0.33 0.21 1.00 0.59 0.60 1.00 rs41923525
GH1 19 GH37 49693285 C > G 0.29 0.15 0.96 0.54 0.58 1.00 rs41923524
   GH36 49693316 G > C 0.29 0.40 1.00 0.52 0.38 1.00 rs41923523
   GH35 49693328 G > A 0.30 0.35 1.00 0.55 0.29 0.96 rs41923522
   GH34 49693374 C > G 0.34 0.33 1.00 0.61 0.53 1.00 rs41923521
   GH32 49693442 A > G 0.67 0.58 1.00 0.39 0.37 1.00 rs196301608
   GH31 49693460 C > T 0.67 0.62 1.00 0.39 0.28 1.00 rs196003442
   GH30 49693512 A > G 0.66 0.65 1.00 0.38 0.38 1.00 rs196003441
   GH29 49693686 C > T 0.50 0.26 0.36 0.50 0.64 0.96 rs41923520
   rs29012855 71150007 C > T 0.99 1.00 1.00 0.90 0.93 1.00 rs29012855
   IGF1i3 71175747 T > C 0.17 0.24 0.95 0.01 0.00 1.00 rs109557731
IGF1 5 IGF1i2 71175753 A > G 0.49 0.46 1.00 0.25 0.15 0.70 rs109227434
   IGF1i1 71176219 A > T 0.26 0.16 1.00 0.37 0.25 1.00 rs110076130
   AF017143 71198324 G > A 0.35 0.26 0.96 0.62 0.76 0.92 AF017143
IGF2 29 IGF2_B_6646 51250879 A > G 0.40 0.40 1.00 0.65 0.47 0.83 rs42196909
   IGF2R_D_41515 100112956 A > G 0.87 0.79 1.00 0.87 0.87 1.00 rs41623543
IGF2R 9 IGF2R_D_41092 100113379 G > A 0.63 0.65 1.00 0.77 0.47 0.22 rs41623544
   IGF2R:g.86262 100134604 G > A 0.86 0.76 0.73 0.86 1.00 0.62 n/a
  1. 1: SNP details according to previous studies [4, 5, 7, 31, 32]; 2: Reported from the forward strand; 3: Allele frequencies represents second allele; 4: Benjamini and Hochberg corrected P values; 5:Genbank accession or dbSNP reference (http://www.ncbi.nlm.nih.gov/projects/SNP/ accessed 9th September 2011).