Table 9.
Clinically Relevant Variants Identified by Whole Genome Sequencing That Were Not Detected by Targeted Next-Generation Sequencing Testing
| Patient ID | Gene | Zygosity | cDNA | Protein | Genomic Coordinates (hg19) |
|---|---|---|---|---|---|
| Large Deletions | |||||
| 12002355 | PCDH15 | Heterozygous | c.-189197_c.610-5166del | Removes start codon | Chr10:56,094,632-56,613,219 |
| 065240 | MERTK | Homozygous | c.-8163_c.1145-1213del | Removes start codon | Chr2:112,648,150-112,739,206 |
| 11012351 | GPR98 | Heterozygous | c.16079-1455_c.16196+155del | p.(Ser5361Profs∗25) | Chr5:90,109,981-90,111,708 |
| 12008422 | USH2A | Heterozygous | c.6326-3582_6658-1028del | p.(Asp2109Glyfs∗11) | Chr1:216,167,537-216,177,486 |
| 067429 | RPGRIP1 | Heterozygous | c.2710+485_3238+810del | p.(Gly904_Asn1079del) | Chr14:21,794,817-21,799,356 |
| Intronic Variants | |||||
| 09006916 | ABCA4 | Heterozygous | c.5461-10T>C | n/a | Chr1:94,476,951 |
| 12007903 | ABCA4 | Heterozygous | c.5461-10T>C | n/a | Chr1:94,476,951 |
| 11012351 | GPR98 | Heterozygous | c.1239-8C>G | n/a | Chr5:89,924,371 |
| Insertions-Deletions | |||||
| 11001193 | PDE6B | Heterozygous | c.1923_1969delinsTCTGGG | p.(Asn643Glyfs∗29) | Chr4:654,564-657,607 |
| 11013807 | USH2A | Heterozygous | c.5614delinsTTAACTTGGCAT | p.(Ala1872Metfs∗4) | Chr1:216,246,601 |
| 12003183 | CRX | Heterozygous | c.648delC | p.(Ser216Argfs∗3) | Chr19:48342972 |
| Missed by Informatics Errors | |||||
| 065238 | ABCA4 | Heterozygous | c.5714+5G>A | n/a | Chr1:94,476,351 |
| 13012708 | ABCA4 | Heterozygous | c.5714+5G>A | n/a | Chr1:94,476,351 |
| Variants in Additional 75 Genes | |||||
| 11012959 | TRPM1 | Homozygous | c.707T>C | p.(Leu236Pro) | Chr15:31,358,296 |
n/a = not available.
∗
Indicates a premature termination during protein translation. All variant confirmations are available online in Figures 4 to 17, available at www.aaojournal.org.