Targeted Genes and Methodology Details for Epilepsy/Seizure Genetic Panels
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1 Targeted s and Methodology Details for Epilepsy/Seizure tic Panels Reference transcripts based on build GRCh37 (hg19) interrogated by Epilepsy/Seizure tic Panels Epilepsy Expanded Panel Epilepsy Expanded Panel ABAT NM_ CPA6 NM_ ACY1 NM_ CPT2 NM_ ADGRG1 NM_ CRH NM_ ADSL NM_ CSTB NM_ AFG3L2 NM_ CTSD NM_ ALDH7A1 NM_ CTSF NM_ ALG13 NM_ CUL4B NM_ AMT NM_ D2HGDH NM_ ARFGEF2 NM_ DCX NM_ ARHGEF9 ARX ASAH1 ATP13A2 ATP1A2 ATP6AP2 ATRX BCKDK BOLA3 CACNA1A CACNA2D2 CASK CDKL5 CERS1 CHD2 CHRNA2 CHRNA4 CHRNB2 CLCN4 CLN3 CLN5 CLN6 CLN8 CNTNAP2 COG7 COG8 COL18A1 COL4A1 COQ9 NM_015185, NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ ENST NM_ NM_ DEPDC5 DNAJC5 DNM1 DOCK7 DYRK1A EEF1A2 EPM2A FARS2 FASTKD2 FGD1 FGFR3 FH FKRP FKTN FLNA FOLR1 FOXG1 GABRA1 GABRB2 GABRB3 GABRD GABRG2 GAMT GATM GCK GFM1 GLUL GNAO1 GOSR2 GPC3 NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ Mayo Foundation for Medical Education and Research Page 1 of 10
2 Page 2 of 10 Epilepsy Expanded Panel GRIA3 NM_ GRIN1 NM_ GRIN2A NM_ GRIN2B NM_ GRN NM_ HCFC1 NM_ HCN1 NM_ HSD17B10 NM_ IBA57 NM_ IER3IP1 NM_ KANSL1 NM_ KCNB1 NM_ KCNC1 NM_ KCNH5 NM_ KCNJ10 NM_ KCNQ2 NM_ KCNQ3 NM_ KCNT1 NM_ KCTD7 NM_ KDM5C NM_ LAMA2 NM_ LARGE1 NM_ LGI1 NM_ MBD5 NM_ MECP2 NM_004992, NM_ MEF2C NM_ MFSD8 NM_ MOCS1 NM_005943, NM_ MOCS2 NM_176806, NM_ MRPL12 NM_ NECAP1 NM_ NEU1 NM_ NHLRC1 NM_ NOTCH3 NM_ NPRL2 NM_ NPRL3* NM_ NR2F1 NM_ NRXN1 NM_ OCLN NM_ OFD1 NM_ OPHN1 NM_ Epilepsy Expanded Panel PAFAH1B1 NM_ PAK3 NM_ PCDH19 NM_ PDSS2 NM_ PEX7 NM_ PHF6 NM_ PHGDH NM_ PIGA NM_ PIGO NM_ PIGV NM_ PLCB1 NM_ PLP1 NM_ PNKP NM_ PNPO NM_ POLG NM_ POMGNT1 NM_ POMT1 NM_ POMT2 NM_ PPT1 NM_ PQBP1 NM_ PRICKLE1 NM_ PRRT2 NM_ PURA NM_ QARS NM_ RAB39B NM_ RAB3GAP1 NM_ RELN NM_ RMND1 NM_ ROGDI NM_ SCARB2 NM_ SCN1B NM_ SCN2A NM_ SCN8A NM_ SCN9A NM_ SERPINI1 NM_ SETBP1 NM_ SIK1 NM_ SLC13A5 NM_ SLC19A3 NM_ SLC25A22 NM_ SLC2A1 NM_ SLC35A2 NM_ SLC6A8 NM_005629
3 SLC9A6 SMC1A SMS SNAP29 SPR SPTAN1 SRPX2 ST3GAL3 ST3GAL5 STX1B STXBP1 SYNGAP1 SYP SZT2 TBC1D24 TCF4 TPP1 TSC1 TSC2 TUBA1A TUBA8 TUBB2B TWNK UBE3A VARS2 VLDLR WDR45 WDR62 WWOX ZEB2 Epilepsy Expanded Panel NM_006359, NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ There are regions of the OCLN gene that cannot be effectively amplified and sequenced due to regions of homology. There are regions of the AFLG3L2, CERS1, COL18A1, COL4A1, CTSF, GABRD, KANSL1, MOCS1, NOTCH3, OCLN, PEX7, SCN1B, and SYNGAP1 genes that cannot be effectively analyzed for the presence of large deletions and/or duplications as a result of technical limitations of the assay, including regions of homology, high GC-rich content, and repetitive sequences. Multiplex Ligation-Dependent Probe Amplification (MLPA), PCR, and/or Sanger sequencing is used to confirm alterations detected by NGS when appropriate. (Unpublished Mayo method) *Reference transcript based on build GRCh38 (hg38) for the NPRL3 gene. Page 3 of 10
4 Page 4 of 10 Encephalopathy with Seizures Panel ABAT NM_ ACY1 NM_ ADSL NM_ ALDH7A1 NM_ AMT NM_ ARFGEF2 NM_ ARHGEF9 NM_015185, NM_ ARX NM_ ATP6AP2 NM_ ATRX NM_ BCKDK NM_ BOLA3 NM_ CACNA2D2 NM_ CASK NM_ CDKL5 NM_ CHD2 NM_ CLCN4 NM_ CLN3 NM_ CLN5 NM_ CLN6 NM_ CLN8 NM_ CNTNAP2 NM_ COG7 NM_ COG8 NM_ COQ9 NM_ CSTB NM_ CTSD NM_ CTSF NM_ CUL4B NM_ D2HGDH NM_ DCX NM_ DNM1 NM_ DOCK7 NM_ EEF1A2 NM_ EPM2A NM_ FARS2 NM_ FASTKD2 NM_ FGD1 NM_ FH NM_ FOLR1 NM_ FOXG1 NM_ GABRA1 NM_ GABRB3 NM_ Encephalopathy with Seizures Panel GABRG2 NM_ GAMT NM_ GCK NM_ GFM1 NM_ GLUL NM_ GNAO1 NM_ GOSR2 NM_ GPC3 NM_ GRIA3 NM_ GRIN1 NM_ GRIN2A NM_ GRIN2B NM_ HCFC1 NM_ HCN1 NM_ HSD17B10 NM_ IBA57 NM_ IER3IP1 NM_ KCNB1 NM_ KCNH5 NM_ KCNJ10 NM_ KCNQ2 NM_ KCNQ3 NM_ KCNT1 NM_ KCTD7 NM_ KDM5C NM_ MBD5 NM_ MECP2 NM_004992, NM_ MEF2C NM_ MFSD8 NM_ MOCS1 NM_005943, NM_ MOCS2 NM_176806, NM_ MRPL12 NM_ NECAP1 NM_ NHLRC1 NM_ NRXN1 NM_ OCLN NM_ OFD1 NM_ OPHN1 NM_ PAK3 NM_ PCDH19 NM_ PDSS2 NM_020381
5 PHF6 PHGDH PIGO PLCB1 PLP1 PNKP PNPO POLG PPT1 PQBP1 PURA RAB39B RMND1 ROGDI SCARB2 SCN1B SCN2A SCN8A SCN9A SERPINI1 SLC13A5 SLC19A3 SLC25A22 SLC2A1 SLC35A2 SLC9A6 SMC1A SMS SPR SPTAN1 SRPX2 ST3GAL3 ST3GAL5 STXBP1 SYNGAP1 SYP SZT2 TBC1D24 TPP1 TSC1 TSC2 TWNK Encephalopathy with Seizures Panel NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_006359, NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ VARS2 WWOX Encephalopathy with Seizures Panel NM_ NM_ There are regions of the OCLN gene that cannot be effectively amplified and sequenced due to regions of homology. There are regions of the CTSF, MOCS1, OCLN, SCN1B, and SYNGAP1 genes that cannot be effectively analyzed for the presence of large deletions and/or duplications as a result of technical limitations of the assay, including regions of homology, high GC-rich content, and repetitive sequences. Multiplex Ligation-Dependent Probe Amplification (MLPA), PCR, and/or Sanger sequencing is used to confirm alterations detected by NGS when appropriate. (Unpublished Mayo method) Page 5 of 10
6 Page 6 of 10 Early Epileptic Encephalopathy Panel ACY1 NM_ ADSL NM_ ALDH7A1 NM_ ALG13 NM_ ARFGEF2 NM_ ARHGEF9 NM_015185, NM_ ARX NM_ ATP6AP2 NM_ BCKDK NM_ CACNA1A NM_ CDKL5 NM_ CHD2 NM_ CLN3 NM_ CLN5 NM_ CLN6 NM_ CLN8 NM_ CNTNAP2 NM_ CSTB NM_ CTSD NM_ CTSF NM_ DNM1 NM_ DYRK1A NM_ EEF1A2 NM_ EPM2A NM_ FARS2 NM_ FOLR1 NM_ FOXG1 NM_ GABRA1 NM_ GABRB2 NM_ GABRB3 NM_ GABRG2 NM_ GAMT NM_ GATM NM_ GOSR2 NM_ GRIN1 NM_ GRIN2A NM_ GRIN2B NM_ KANSL1 NM_ KCNB1 NM_ KCNJ10 NM_ KCNQ2 NM_ KCNQ3 NM_ KCNT1 NM_ Early Epileptic Encephalopathy Panel KCTD7 NM_ MBD5 NM_ MECP2 NM_004992, NM_ MEF2C NM_ MFSD8 NM_ NHLRC1 NM_ NR2F1 NM_ NRXN1 NM_ PCDH19 NM_ PIGA NM_ PIGO NM_ PIGV NM_ PLCB1 NM_ PNKP NM_ PNPO NM_ POLG NM_ PPT1 NM_ PRRT2 NM_ QARS NM_ ROGDI NM_ SCARB2 NM_ SCN1B NM_ SCN2A NM_ SCN8A NM_ SCN9A NM_ SETBP1 NM_ SIK1 NM_ SLC19A3 NM_ SLC25A22 NM_ SLC2A1 NM_ SLC6A8 NM_ SLC9A6 NM_006359, NM_ SPTAN1 NM_ ST3GAL3 NM_ ST3GAL5 NM_ STXBP1 NM_ SZT2 NM_ TBC1D24 NM_ TCF4 NM_ TPP1 NM_ TSC1 NM_000368
7 TSC2 UBE3A WDR45 WWOX ZEB2 Early Epileptic Encephalopathy Panel NM_ NM_ NM_ NM_ NM_ There are regions of the CTSF, KANSL1, and SCN1B genes that cannot be effectively analyzed for the presence of large deletions and/or duplications as a result of technical limitations of the assay, including regions of homology, high GC-rich content, and repetitive sequences. Multiplex Ligation-Dependent Probe Amplification (MLPA), PCR, and/or Sanger sequencing is used to confirm alterations detected by NGS when appropriate. (Unpublished Mayo method) Neuronal Migration Disorders Panel ADGRG1 NM_ ARFGEF2 NM_ ARX NM_ COL18A1 ENST COL4A1 NM_ CPT2 NM_ DCX NM_ DEPDC5 NM_ FGFR3 NM_ FKRP NM_ FKTN NM_ FLNA NM_ LAMA2 NM_ LARGE1 NM_ PAFAH1B1 NM_ PEX7 NM_ POMGNT1 NM_ POMT1 NM_ POMT2 NM_ PQBP1 NM_ RAB3GAP1 NM_ RELN NM_ SNAP29 NM_ SRPX2 NM_ TUBA1A NM_ TUBA8 NM_ TUBB2B NM_ VLDLR NM_ WDR62 NM_ There are regions of the COL18A1, COL4A1, and PEX7 genes that cannot be effectively analyzed for the presence of large deletions and/or duplications as a result of technical limitations of the assay, including regions of homology, high GC-rich content, and repetitive sequences. Page 7 of 10
8 Progressive Myoclonic Epilepsy Panel AFG3L2 NM_ ASAH1 NM_ ATP13A2 NM_ CERS1 NM_ CLN3 NM_ CLN5 NM_ CLN6 NM_ CLN8 NM_ CSTB NM_ CTSD NM_ CTSF NM_ DNAJC5 NM_ EPM2A NM_ FOLR1 NM_ GOSR2 NM_ GRN NM_ KCNC1 NM_ KCTD7 NM_ MFSD8 NM_ NEU1 NM_ NHLRC1 NM_ PPT1 NM_ PRICKLE1 NM_ SCARB2 NM_ SERPINI1 NM_ TBC1D24 NM_ TPP1 NM_ There are regions of the AFLG3L2, CERS1, and CTSF genes that cannot be effectively analyzed for the presence of large deletions and/or duplications as a result of technical limitations of the assay, including regions of homology, high GC-rich content, and repetitive sequences. Page 8 of 10
9 ALDH7A1 ARFGEF2 ARX CDKL5 COL4A1 FOXG1 GABRB3 GRIN2A MEF2C PNPO SCN2A SLC25A22 SLC2A1 SPTAN1 STXBP1 TSC1 TSC2 Infantile Spasms Panel NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ There are regions of the COL4A1 gene that cannot be effectively analyzed for the presence of large deletions and/or duplications as a result of technical limitations of the assay, including regions of homology, high GC-rich content, and repetitive sequences. Focal Epilepsy Panel CHRNA2 NM_ CHRNA4 NM_ CHRNB2 NM_ CNTNAP2 NM_ CRH NM_ DEPDC5 NM_ FLNA NM_ GRIN2A NM_ KCNT1 NM_ LGI1 NM_ NPRL2 NM_ NPRL3* NM_ PRRT2 NM_ SCN1B NM_ SRPX2 NM_ *Reference transcript based on build GRCh38 (hg38) for the NPRL3 gene. There are regions of the SCN1B gene that cannot be effectively analyzed for the presence of large deletions and/or duplications as a result of technical limitations of the assay, including regions of homology, high GC-rich content, and repetitive sequences. Page 9 of 10
10 CPA6 GABRD GABRG2 PCDH19 SCN1B SCN2A SCN9A STX1B Febrile Seizure Panel NM_ NM_ NM_ NM_ NM_ NM_ NM_ NM_ There are regions in GABRD and SCN1B that cannot be effectively analyzed for the presence of large deletions and/or duplications as a result of technical limitations of the assay, including regions of homology, high GC-rich content, and repetitive sequences. ATP1A2 CACNA1A NOTCH3 POLG PRRT2 SLC2A1 Epilepsy with Migraine Panel NM_ NM_ NM_ NM_ NM_ NM_ There are regions in NOTCH3 that cannot be effectively analyzed for the presence of large deletions and/or duplications as a result of technical limitations of the assay, including regions of homology, high GC-rich content, and repetitive sequences. TSC1 TSC2 Tuberous Sclerosis Panel NM_ NM_ Page 10 of 10
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