Summary of Loci and Number of Discordant Typings
| Locus | Chr.location | Conven-tional method[i] | G/C content (%)[ii] | Homology to Chr. 22 (bK246H3) (%)[iii] | Homology to repeat elements | Total Discord.[iv] | Conventional assay[v] | Invader assay[v] | Failure rate | Total discord.between 96- and 384-well formats | |||
| no. false hets | no. false homs | no. false hets | no.false homs | 96-well format (%) | 384-well format (%) | ||||||||
| INSg.-23A>T | 11p15 | RFLP (HphI) | 65 | — | 8 | 3 | 5 | 0.8 | |||||
| INSg.1127C>T | 11p15 | RFLP (PstI) | 67 | — | 0 | 1.3 | |||||||
| LRP5g.-14279A>G | 11q13 | cRFLP (NruI) | 61 | 0 | 7 | 1 | 6 | 2.6 | |||||
| LRP5g.-11215T>A | 11q13 | N.T. | 30 | 0 | AluY | N.T. | 2.6 | ||||||
| LRP5g.-11094G>A | 11q13 | RFLP (BstX1) | 61 | 0 | AluY | 2 | 1 | 1 | 1.8 | ||||
| LRP5g.-10088G>A | 11q13 | RFLP (FauI) | 59 | 0 | 13 | 7 | 6 | 1.0 | 3.4 | 0 | |||
| LRP5g.-9693G>A | 11q13 | RFLP (Acil) | 59 | 0 | 1 | 1 | 1.3 | 2.9 | 2 | ||||
| LRP5g.-5802G>C | 11q13 | RFLP (HincII) | 56 | 93 | 1 | 1 | 1.8 | 2.6 | 1 | ||||
| LRP5g.-5677C>T | 11q13 | RFLP (MspI) | 48 | 97 | AluSp | 2 | 2 | 3.4 | 1.6 | 0 | |||
| LRP5g.-5264G>A | 11q13 | RFLP (AfIII) | 51 | 93 | AluJb | 2 | 2 | 2.1 | 2.3 | 0 | |||
| LRP5g.-864A>G | 11q13 | RFLP (MspI) | 63 | 89 | 6 | 2 | 1 | 3 | 2.6 | 2.3 | 1 | ||
| LRP5g.2221C>T | 11q13 | cRFLP (Hph) | 48 | 92 | 8 | 1 | 7 | 4.9 | |||||
| LRP5g.3103C>G | 11q13 | RFLP (PflMI) | 56 | 97 | 0 | 1.8 | |||||||
| LRP5g.4780G>C | 11q13 | RFLP (EcoNI) | 64 | 58 | 8 | 1 | 7 | 3.4 | |||||
| LRP5g.5257T>G | 11q13 | cRFLP (SnaBI) | 36 | 69 | 4 | 2 | 2 | 2.6 | |||||
| LRP5g.7374G>A | 11q13 | RFLP (AvaI) | 50 | 83 | AluJb | 7 | 1 | 6 | 2.9 | ||||
| LRP5g.13963C>T | 11q13 | N.T. | 66 | 79 | N.T. | 1.8 | |||||||
| LRP5g.24964C>T | 11q13 | RFLP (MnlI) | 59 | 0 | 1 | 1 | 1.0 | ||||||
| LRP5g.28149C>T | 11q13 | RFLP (MboII) | 44 | 0 | 2 | 2 | 1.6 | ||||||
| LRP5g.31856G>A | 11q13 | RFLP (DpnI) | 60 | 0 | AluSx | 3 | 1 | 1 | 1 | 0.5 | |||
| LRP5g.35592T>C | 11q13 | N.T. | 54 | 0 | N.T. | 2.6 | |||||||
| LRP5g.42125G>T | 11q13 | N.T. | 49 | 0 | N.T. | 1.0 | |||||||
| LRP5g.45704G>A | 11q13 | N.T. | 61 | 92 | AluJb | N.T. | 1.3 | ||||||
| EST3c.448G>A | 11q13 | RFLP (PstI) | 57 | — | 1 | 1 | 5.7 | ||||||
| EST4c.3021-3026del | 11q13 | Length polymorph. | 24 | — | 0 | 7.3 | 5.2 | 0 | |||||
| EST4c.3211G>A | 11q13 | cRFLP (NlaIII) | 31 | — | 0 | 3.6 | 3.4 | 0 | |||||
| EST4c.3403G>A | 11q13 | N.T. | 34 | — | N.T. | 1.8 | 3.6 | 0 | |||||
| IL4-Rc.1216T>C | 16p12 | RFLP (Tsp45I) | 59 | — | 3 | 1 | 1 | 1 | 1.8 | ||||
| IL4-Rc.1902A>G | 16p12 | ARMs | 66 | — | 2 | 1 | 1 | 0.5 | |||||
| GCG-R G40S | 17q25 | RFLP (BstEII) | 54 | — | 0 | 6.0 | |||||||
| ICAM-1 G241R | 19p13 | cRFLP (Stu1)/ARMS | 67 | — | 7 | 1 | 6 | 1.6 | |||||
| ICAM-1 K469E | 19p13 | RFLP (MvnI)/ARMS | 60 | — | 4 | 1 | 3 | 1.0 | |||||
| CTLA4g.-651C>T | 2q33 | RFLP (Acil) | 34 | — | 0 | 2.6 | |||||||
| CTLA4g.49A>G | 2q33 | RFLP (Bbvl)/dot blot | 56 | — | 5[vi] | 1 | 2 | 1 | 1.0 | ||||
| CTLA4g.920C>T | 2q33 | RFLP (DdeI) | 38 | — | 1 | 1 | 1.0 | ||||||
| CTLA4g.-318C>T | 2q33 | RFLP (MseI) | 24 | — | 0 | 0.8 | |||||||
| IRS1 G972R | 2q36 | RFLP (SmaI) | 68 | — | 0 | 4.9 | |||||||
| Total | 98 | 19 | 26 | 4 | 49 | 4 | |||||||
| Error rate (%) | 0.82 | 0.16 | 0.22 | 0.03 | 0-.41 | 2.34 | 3.03 | 0.12 | |||||
[i] (N.T.) The locus was not typed conventionally.
[ii] Percentage of bases with G or C 35 bp either side of the SNP.
[iii] Percentage of bases homologous to bac 6K246H3 35 bp either side of the polymorphism.
[iv] Number of individuals discordant between the two typing methods after a single typing. (N.T.) Not tested.
[v] Outcome of repeat typing. Each discordant individual was typed at least 4 times, twice with each technology. In all but one case a consensus genotype was established and one initial typing was incorrect.
[vi] A single individual consistantly typed as heterozygote with Invader technology but homozygote with PCR–RFLP.