Table 2.
Missing disease-causing variants
| Individual (gene) | Inheritance | Prior genetic testing | Known variant identified by T-LRS | Missing variant identified by T-LRS | Category of variant | ACMG criteria met | Confirmation |
|---|---|---|---|---|---|---|---|
| S002 (ALMS1) | AR | SNP, ES, ELA | p.Ser745∗ | Alu insertion in exon 20 | P | PVS1, PM3, PP4 | clinically confirmed |
| S003 (NPHP4) | AR | SNP, ES, ELA | p.Gln45∗ | NM_015102.4:c.517+50C>G; splice site variant | P | PS3, PM2, PM3, PP3, PP4 | confirmed to affect splicing by RT-qPCR |
| S004 (VARS2) | AR | SNP, ES, ELA | p.Ala420Thr | none identified | – | – | – |
| S008 (HPRT1) | X-linked | karyotype, TS of HPRT1 | N/A | 17 Mbp paracentric inversion bisecting HPRT1 | P | PVS1 | clinically confirmed |
| S009 (DMD) | X-linked | SNP, ELA, TS of DMD | N/A | AGAA expansion in intron 16 | VUS | PM2 | observed in mother and absent in unaffected brother of proband |
| S013 (HPS1) | AR | SNP, ES | p.Arg439∗ | ~1,900 bp deletion that includes exon 3 (first coding exon) | LP | PVS1, PM3 | clinically confirmed |
| S018 (PAH) | AR | PKU panel | c.1066−11G>A | none identified | – | – | – |
| S025 (ABCA4) | AR | SNP, ES, research WGS | p.Arg1108Cys | ~1,500 bp transposable element insertion in intron 1 | VUS | PM3, PP3, PP4 | confirmed by reanalysis of short-read WGS |
| S047 (AGL) | AR | TS of AGL, research WGS | p.Val426∗ | 1,525 bp deletion including part of exon 3 | P | PVS1 | confirmed by reanalysis of short-read WGS data |
| S056 (WDR19) | AR | ciliopathy panel, ELA | p.Arg1178Gln | NM_025132.3:c.1250-197C>T; splice site variant | LP | PM2, PM3, PP3, PP4 | variant confirmed by PCR |
In eight of ten individuals with suspected genetic diseases, T-LRS identified six pathogenic or likely pathogenic disease-causing variants and two variants of uncertain clinical significance not identified by clinical or research testing. Prior testing of individual S009 included a muscle biopsy and immunohistochemistry, which found minimal dystrophin present.
AR, autosomal recessive; SNP, single-nucleotide polymorphism array; ELA, exon-level array; ES, exome sequencing; TS, targeted sequencing; PKU, phenylketonuria; P, pathogenic; LP, likely pathogenic; VUS, variant of uncertain significance; RT-qPCR, reverse transcription quantitative PCR; WGS, whole-genome sequencing.