Table 2. Information about the MYH9 non-coding SNPs and the non-synonymous APOL1 SNPs, genotyped in this study.
SNP | Risk haplotype | Forward primer | Reverse primer | Tm (°C) | Restriction enzyme | Cleavage products (bp) | Known associations in Caucasian populations |
MYH9 rs4821481 (T/C) | E1 | GAAGAGTACCCCGTATCTCAACAC | AGCATGAGGGCTTCTGCTTAACT | 65 | BfaI | 132+115 (T allele) | 1. Non-diabetic ESKD in Hispanic Americans [26] 2. Diabetic nephropathy in European Americans [33] |
MYH9 rs4821480 (T/G) | E1 | CTCATGCTTGTTCTTGAGCTTG | AGAACAGAAAGCAAGGAGAGCAG | 66 | DraI | 261+291 (T allele) | 1. Non-diabetic ESKD in Hispanic Americans [26] 2. Diabetic nephropathy in European Americans [33] 3. Non-diabetic CKD in European Americans [33] |
MYH9 rs2413396 * (T/C) | S1 | CCAGCACCTCCCCGTGA | GTGGAGAAGGTGATGCAGGAG | 65 | HaeII | 109+21 (C allele) | 1. Non-diabetic ESKD in Hispanic Americans [33] |
MYH9 rs11089788 (C/A) | No strong LD (<0.3) with any neighboring SNPs, according to HapMap data | GATGTCCCATCCAATTGTTTTC | GATTATGGCCTAAAAAGGCAACTG | 59 | BslI | 230+158 (C allele) | 1. Association with serum creatinine levels in three Caucasian populations [33] |
APOL1 E149K | - | CTGGTTTCTGAAAGAGTTTCCTCGGTTGAAAATT ** | GCTGTGATTCCCAACTCCATCCCAGGTTCCAA | 60 | MseI | 207+33 (K allele) | - |
APOL1 M227I | - | CGTATTAGTCAGGATGGTCTCAATC | AAAGTTGGATATGTTCTCACCCAAA | 65 | BtgI | 505+115 (M allele) | - |
APOL1 R254K | - | CTGGTCATCAAAAGCCTTGACAAATTGAAGGAGGTTA ** | ATTAACCCTCTCCACCTGTTCACCGCTTTCAGCTG | 67 | MseI | 201+35+4 (K allele) | - |
Genotyping of rs2413396 was performed according to [27].
Modified nucleotides for creating restriction sites are in bold and underlined.