Table 3.
Comparison of the results of NGS and previous DNA analysis
| Genotype by Sanger sequencing or restriction digest | Detected by NGS | Variant reads (%) | Variant effect | No. of patients |
|---|---|---|---|---|
| PH1 patients | ||||
| c.2_3delinsAT; c.33dupC | Yes; Yes | 73;26 | p.Met1Asn; p.Lys12fs | 1 |
| c.32_33delCC; c.1045G>A | Yes; Yes | 30;62 | p.Pro11fs; p.Gly349Ser | 1 |
| c.33dupC; c.33dupC | Yes; Yes | 96 | p.Lys12fs; p.Lys12fs | 3 |
| c.33dupC; c.454T>A | Yes; Yes | 53;47 | p.Lys12fs; p.Phe152Ile | 1 |
| c.33dupC; c.508G>A | Yes; Yes | 52;29 | p.Lys12fs; p.Gly170Arg | 2 |
| c.33dupC; c.547G>A | Yes; Yes | 46;51 | p.Lys12fs; p.Asp183Asn | 1 |
| c.33dupC; c.846G>C | Yes; Yes | 44;56 | p.Lys12fs; p.Gln282His | 1 |
| c.33dupC; c.886_888delGCG | Yes; Yes | 48;49 | p.Lys12fs; p.Ala296del | 1 |
| c.302T>C; c.302T>C | Yes; Yes | 100 | p.Leu101Pro; p.Leu101Pro | 1 |
| c.423G>T; c.423G>T | Yes; Yes | 97 | p.Glu141Asp; p.Glu141Asp | 1 |
| c.447_454delGCTGCTGT; c.447_454delGCTGCTGT; | Yes; Yes | 100 | p.Leu151fs; p.Leu151fs | 2 |
| c.481G>T; c.614C>T | Yes; Yes | 25;53 | p.Gly161Cys; p.Ser205X | 1 |
| c.508G>A; c.106C>T | Yes; Yes | 49;41 | p.Gly170Arg; p.Arg36Cys | 1 |
| c.508G>A; c.116_117dupCA | Yes; Yes* | 44;99 | p.Gly170Arg; p.Ala40fs | 1 |
| c.508G>A; c.121G>A | Yes; Yes* | 46;95 | p.Gly170Arg; p.Gly41Arg | 2 |
| c.508G>A; c.209C>A | Yes; Yes | 49;54 | p.Gly170Arg; p.Thr70Asn | 1 |
| c.508G>A; c.215dupA | Yes; Yes | 45;56 | p.Gly170Arg; p.Asn72fs | 1 |
| c.508G>A; c.322T>C | Yes; Yes | 49;35 | p.Gly170Arg; p.Trp108Arg | 1 |
| c.508G>A; c.454T>A | Yes; Yes | 55;49 | p.Gly170Arg; p.Phe152Ile | 2 |
| c.508G>A; c.508G>A | Yes; Yes | 99 | p.Gly170Arg; p.Gly170Arg | 4 |
| c.508G>A; c.533G>A | Yes; Yes | 44;47 | p.Gly170Arg; p.Cys178Tyr | 1 |
| c.508G>A; c.577dupC | Yes; Yes | 46;47 | p.Gly170Arg; p.Leu193fs | 1 |
| c.508G>A; c.653C>T | Yes; Yes | 52;64 | p.Gly170Arg; p.Ser218Leu | 1 |
| c.508G>A; c.697C>T | Yes; Yes | 50;43 | p.Gly170Arg; p.Arg233Cys | 1 |
| c.508G>A; c.731T>C | Yes; Yes | 46;47 | p.Gly170Arg; p.Ile244Thr | 1 |
| c.508G>A; c.738G>A | Yes; Yes | 45;48 | p.Gly170Arg; p.Trp246X | 1 |
| c.508G>A; c.847-3C>G | Yes; Yes | 49;48 | p.Gly170Arg; mis-splicing | 2 |
| c.508G>A; c.943-1G>T | Yes; Yes | 46;52 | p.Gly170Arg; mis-splicing | 1 |
| c.508G>A; c.996G>A | Yes; Yes | 45;17 | p.Gly170Arg; p.Trp332X | 1 |
| c.508G>A; unk | Yes; unk | 49 | p.Gly170Arg; unk | 1 |
| c.508G>A; c.473delC | Yes; Yes | 57;40 | p.Gly170Arg; p.Ser158fs | 1 |
| c.508G>A; c.1076T>C | Yes; Yes | 47;57 | p.Gly170Arg; p.Leu359Pro | 1 |
| c.560C>T; c.560C>T | Yes; Yes | 100 | p.Ser187Phe; p.Ser187Phe | 1 |
| c.577dupC; c.847-3C>G | Yes; Yes | 51;47 | p.Leu193fs; mis-splicing | 1 |
| c.568G>A; c.568G>A | Yes; Yes | 99 | p.Gly190Arg; p.Gly190Arg | 2 |
| c.584T>G; c.584T>G | Yes; Yes | 100 | p.Met195Arg; p.Met195Arg | 1 |
| c.661T>C; c.661T>C | Yes; Yes | 98 | p.Ser221Pro; p.Ser211Pro | 1 |
| c.680+2T>A; c.346G>A | Yes; No | 58;10 | Mis-splicing; p.Gly116Arg | 1 |
| c.697C>T; c.697C>T | Yes; Yes | 100 | p.Arg233Cys; p.Arg233Cys | 1 |
| c.698G>A; c.466G>A | Yes; Yes | 55;80 | p.Arg233His; p.Gly156Arg | 1 |
| c.698G>A; c.603C>A | Yes; Yes | 55;53 | p.Arg233His; p.Asp201Glu | 1 |
| c.731T>C; c.248A>G | Yes; Yes | 48;54 | p.Ile244Thr; p.His83Arg | 1 |
| c.731T>C, c.731T>C | Yes; Yes | 99 | p.Ile244Thr; p.Ile244Thr | 3 |
| c.731T>C; c.847-3C>G | Yes; Yes | 45;54 | p.Ile244Thr; mis-splicing | 1 |
| c.798_802 delinsACAATCTCAG; c.798_802 delinsACAATCTCAG | Yes; Yes | 100 | p.Ile267fs; p.Ile267fs | 1 |
| c.822G>C; c.822G>C | Yes; Yes | 99 | p.Glu247Asp; p.Glu247Asp | 1 |
| c.847-1G>A;c.847-1G>A | Yes; Yes | 99 | mis-splicing; mis-splicing | 1 |
| c.976delG; c.976delG | Yes; Yes | 100 | p.Val326fs; p.Val326fs | 1 |
| c.1049G>A; c.1049G>A | Yes; Yes | 99 | p.Gly350Asp; p.Gly350Asp | 1 |
| unk; unk | unk; unk | unk; unk | 1 | |
| PH2 patients | ||||
| c.102G>A;c.965T>C | Yes; Yes | 51;54 | p.Trp34X; p.Met322Thr | 1 |
| c.103delG; c.103delG | Yes; Yes | 100 | p.Asp35fs; p.Asp35fs | 2 |
| c.103delG; c.84-2A>G | Yes; Yes | 51;46 | p.Asp35fs; mis-splicing | 1 |
| c.103delG; c.905G>A | Yes; Yes | 100 | p.Asp35fs; p.Arg302His | 1 |
| c.295C>T; c.493+2T>A | Yes; Yes | 52;55 | p.Arg99X; mis-splicing | 1 |
| c.403_404+2delAAGT; c.403_404+2delAAGT | Yes; Yes | 100 | mis-splicing | 2 |
| c.403_404+2delAAGT; c.540delT | Yes; Yes | 26;34 | mis-splicing | 1 |
| c.45delA;c.45delA | Yes; Yes | 100 | p.Ala17fs; p.Ala17fs | 1 |
| c.494G>A; c.494G>A | Yes; Yes | 100 | p.Gly165Asp; p.Gly165Asp | 3 |
| c.84-2A>G; c.84-2A>G | Yes; Yes | 100 | mis-splicing | 1 |
| PH3 patients | ||||
| c.107C>T; c.860G>T | Yes; Yes | 49;16 | p.Ala36Val; p.Gly287Val | 1 |
| c.346C>T; c.346C>T | Yes; Yes | 96 | p.Gln116X; p.Gln116X | 1 |
| c.700+5G>T; c.158delA | Yes; Yes | 58;28 | mis-splicing; p.Asp53fs | 1 |
| c.700+5G>T; c.208C>T | Yes; Yes | 50;49 | mis-splicing; p.Arg70X | 1 |
| c.700+5G>T; c.700+5G>T | Yes; Yes | 100 | mis-splicing | 3 |
| c.700+5G>T; c.907C>T | Yes; Yes | 56;34 | mis-splicing; p.Arg303Cys | 1 |
| c.860G>T; c.944_946delAGG | Yes; Yes | 16;16 | p.Gly287Val; p.Glu315del | 1 |
| c.875T>C; c.875T>C | Yes; Yes | 100 | p.Met292Thr; p.Met292Thr | 1 |
| c.944_946delAGG; c.944_946delAGG | Yes; Yes | 100 | p.Glu315del; p.Glu315del | 2 |
For variants detected in multiple patients, the mean result is shown for % variant reads. The asterisk (*) indicates the two variants incorrectly assigned as homozygous by the NGS base calling. Novel variants are shown in bold. NGS, next generation sequencing; PH, primary hyperoxaluria.