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Table 1 Flanking regions associated with optimized prediction models for each platform

From: Predicting HLA genotypes using unphased and flanking single-nucleotide polymorphisms in Han Chinese population

    

Flanking region2(SNPs3/total SNPs4(D’)5)

    

Without imputation

With imputation

Gene

Start1

Stop1

Length (bp)

Affy5.0

Affy6.0

Illumina550K

Union

Affy5.0

Affy6.0

Illumina550K

Union

HLA_A

30,018,310

30,021,632

3,322

200 K (14/122 (0.76))

350 K (16/299 (0.69))

150 K (14/121 (0.79))

200 K (16/329 (0.74))

150 K (19/352 (0.81))

150 K (17/364 (0.80))

200 K (17/515 (0.73))

150 K (16/366 (0.80))

HLA_B

31,429,630

31,432,914

3,284

150 K (20/100 (0.61))

100 K (20/123 (0.66))

100 K (18/131 (0.59))

100 K (21/237 (0.64))

100 K (24/282 (0.67))

40 K (21/110 (0.71))

30 K (22/102 (0.71))

40 K (22/110 (0.71))

HLA_C

31,344,509

31,347,834

3,325

150 K (17/104 (0.64))

20 K (14/25 (0.83))

10 K (13/22 (0.82))

30 K (17/95 (0.79))

30 K (19/137 (0.83))

20 K (18/88 (0.85))

20 K (16/88 (0.85))

20 K (18/88 (0.85))

HLA_DPB1

33,151,738

33,162,954

11,216

100 K (13/88 (0.49))

150 K (15/154 (0.47))

100 K (15/120 (0.52))

150 K (18/280 (0.47))

20 K (34/113 (0.79))

100 K (33/352 (0.54))

150 K (35/452 (0.51))

100 K (35/355 (0.54))

HLA_DQB1

32,735,635

32,742,419

6,784

40 K (12/15 (0.61))

40 K (11/30 (0.71))

30 K (12/13 (0.72))

30 K (13/29 (0.70))

30 K (16/52 (0.69))

30 K (16/52 (0.69))

30 K (15/52 (0.69))

30 K (15/52 (0.69))

HLA_DRB1

32,654,527

32,665,559

11,032

200 K (16/108 (0.60))

100 K (16/27 (0.73))

150 K (17/108 (0.61))

150 K (21/204 (0.61))

150 K (25/325 (0.61))

100 K (22/91 (0.76))

200 K (25/523 (0.58))

150 K (24/326 (0.62))

  1. 1Based on NCBI build 36.3.
  2. 2Flanking region for the most accurate prediction model.
  3. 3Number of SNPs within the region that were selected for the model (based on predictive power).
  4. 4Total number of SNPs in the MHC and HLA regions.
  5. 5Hedridge’s multialleic D.