Comprehensive Genetic Testing for Hearing and Vision Loss

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Comprehensive genetic testing for hearing and vision loss

Hearing and vision loss can result from both genetic and non-genetic etiologies

In general, there is a genetic basis for up to 50% of prelingual hearing loss and up to 60% of congenital blindness among infants. Indications for genetic testing for deafness and/or vision loss may include

Clinical status: To confirm a clinical diagnosis in an affected patient, in an individual with unknown status (who has not received screening or evaluation), or in unaffected relatives of an affected patient (who have had normal screenings and/or evaluations). The purpose of the test may be diagnostic, carrier testing, familial follow-up on a known family variant, or prenatal testing for known variant(s)

Treatment: To clarify the cause of hearing and/or vision loss, provide information on the likelihood of related health issues, and guide treatment

Family risk: To establish risk to other family members and future generations. Genetic testing can help family members who are susceptible to certain drugs avoid drug-induced hearing loss. For example, aminoglycoside drugs can cause hearing loss in individuals with mutations in the MT-RNR1 gene. Furthermore, testing can confirm syndromic conditions, enabling early detection and surveillance for defects in other organs

The disorders included in our hearing and vision loss panels may be inherited in an autosomal dominant, autosomal recessive, or X-linked manner

For genes displaying an autosomal dominant mode of inheritance, an affected parent carrying the mutated gene has a 1 in 2 chance of passing the variant on to a child, regardless of gender. Some of these genes are not fully penetrant, meaning that an individual may have a mutated gene. but not display any signs or symptoms of the disorder. Additionally, these disorders may have variable expressivity.

For diseases with autosomal recessive inheritance, there is a 1 in 4 chance of having a child who is affected by the disease if both parents are carriers. The parents of an affected child are most often obligate carriers (heterozygotes) and each carry one mutant allele, unless a de novo mutation occurs.

An X-linked inheritance means that there is a 1 in 2 chance that a male child will be affected by the disorder if the mother carries an X-linked mutation. Depending on the X-inactivation pattern of the gene, a mother and her daughters rarely may be affected. Although X-linked diseases are normally transmitted from mother to son, transmission of an X-linked mutation will occur from an affected father to each daughter, but will not occur from father to son. Genetic testing options for hearing and vision loss

The Comprehensive Hearing and Vision Loss Panel detects pathogenic variants in 308 genes. It encompasses two smaller panels—the Comprehensive Vision Loss Panel and the Comprehensive Hearing Loss Panel.

Comprehensive Hearing and Vision Loss Panel (308 genes)

Comprehensive Hearing Comprehensive Vision Loss Panel (250 genes) Loss Panel (92 genes)

ABCA CNGB1 GCA1B OCA2 RPGR ADGR1 ACTG1 MO1A ABD12 CNGB GC2D OFD1 RPGRIP1 CD2 AIFM1 MOA ADAM CNNM CCS OPA RPGRIP1L CIB2 CACNA1D MO6 AG COL11A1 ESX1 OPN1S RS1 CLRN1 CCDC OTOA AI1 COL2A1 PS1 OTX2 SAG COL11A2 CEACAM16 OTOF AIPL1 COLA1 PS PAN2 SDCCAG8 EDN CLDN1 OTOG ALMS1 COLA2 PS PAX6 SEMAA EDNRB COC OTOGL APB1 CRB1 PS PDE6A SLC2A1 EA1 DFNA P2RX2 ARL1B CRX PS6 PDE6B SLCA2 ARS DFNB POF ARL6 CRAA SF PDE6C SMOC1 MITF DIABLO POF BBS1 CRAB IFT1 PDE6G SNRNP2 M DIAP1 PTPR BBS1 CRBB1 IMPD1 PDE6 SOX2 MOA ESPN RDX BBS12 CRBB IMPG2 PG1 SPATA OPA1 ESRRB SERPINB6 BBS2 CTSD INPPE PITPNM STRA6 PAX EA SIX1 BBS CP1B1 ICB1 PITX2 TCTN1 PCD1 GIPC SIX BBS CP2 JAG1 PITX TCTN2 PEX1 GJB2 SLC26A BBS DDDS CNJ1 PLA2G TCTN PEX1 GJB6 SMPX BBS DNAJC CN2 PPT1 TDRD PEX1 GPSM2 STRC BCOR EFEMP1 IF11 PRCD TGFBI PEX16 GRL2 TBC1D2 BEST1 ELOL IF PROM1 TIMP PEX1 GRXCR1 TECTA BLOC1S6 ERCC6 LL PRPF TMEM216 PEX2 GF TMC1 BMP ES LCA PRPF1 TMEM21 PEX ILDR1 TMIE C2orf1 FAM161A LRAT PRPF6 TMEM2 PEX6 ARS TMPRSS Corf2 FLCR1 LRIT PRPF8 TMEM6 PEX CN1 TPRN C8orf FOXC1 LRP PRP2 TOPORS P CN TRIOBP CA FOXE LST PXDN TPP1 PRPS1 LFPL TSPEAR CABP FRAS1 LTFL1 RAB28 TREX1 SOX1 LOXD1 CACNA1F FREM1 MA RAX2 TRIM2 TIMM8A LRTOMT CACNA2D FREM2 MERT RBP TRPM1 TMEM126A MARELD2 CAPN FRMD MFRP RBP TSPAN12 S1C MSRB CC2D2A FSCN2 MFSD8 RD TTC21B S1G MT-RNR1 CD FCO1 MS RD12 TTC8 S2A M1 CDR1 FD MS1 RD TLP1 FS1 CEP16 GCNT2 MTTP RGR TR RN CEP2 GJA8 MOC RGS TRP1 CEP1 GNAT1 NDP RGSBP BIAD1 CERL GNAT2 NMNAT1 RO CAN CM GNPTG NPP1 RIMS1 SX2 CLN GPR1 NPP RLBP1 DR1 CLN GPR1 NPP ROM1 NF2 CLN6 GRIP1 NR2E RP1 CLN8 GR1 NRL RP1L1 CNGA1 GRM6 NX RP2 CNGA GCA1A OAT RPE6

All genes were selected for inclusion based on literature review, clinical actionability scores, and comparison with commercially available assays. Comprehensive Vision Loss Panel (250 genes)

lbinism, Hermansky-Pudlak yndrome, etinal isease ubpanel (54 genes) and aardenburg yndrome ubpanel (8 genes)

CABP ABCA CRB1 NR2E RO APB1 PS PAX CD ADAM CP2 NRL RIMS1 BLOC1S6 PS SLCA2 CLN ADGR1 DDD2 OFD1 ROM1 EDN PS SOX1 CLN AI1 ES OPA1 RP1 CACNA1F EDNRB PS6 TR CLN6 AIPL1 FAM161A OPN1S RP1L1 GPR1 MITF TRP1 CLN8 ALMS1 FLCR1 PAN2 RP2 PS1 OCA2 CTSD ARL1B FSCN2 PCD1 RPE6 CP1B1 ARL6 GNAT2 PDE6A RPGR ubpanel (2 genes) DNAJC BBS1 GPR1 PDE6B RPGRIP1 evelopmental ye EFEMP1 BBS1 GR1 PDE6C RPGRIP1L ELOL BBS12 GRM6 PDE6G SAG BMP FREM2 PLA2G FRMD BBS2 GCA1A PDE6 SDCCAG8 FOXC1 GRIP1 SMOC1 MFRP FD BBS GCA1B PEX1 SEMAA FOXE CCS SOX2 GNAT1 BBS GC2D PEX1 SLC2A1 FRAS1 1F11 STRA6 ESX1 BBS ARS PEX1 SNRNP2 FREM1 LST BBS IFT1 PEX1 SPATA MFSD8 C2orf1 IMPD1 PEX2 TCTN1 MTTP Corf2 IMPG2 PEX TCTN2 MOC C8orf INPPE PEX6 TCTN BCOR PAX6 SX2 NX CA ICB1 PITPNM TMEM126A NDP PITX PG1 CACNA2D CN2 PRCD TMEM216 OTX2 PXDN PITX2 CC2D2A IF PROM1 TMEM21 PPT1 CD2 LL PRPF TMEM2 RGS CDR1 LCA PRPF1 TMEM6 AG ERCC6 OPA RGSBP CEP16 LRAT PRPF6 TOPORS COL11A1 EA1 PEX RS1 CEP2 LRIT PRPF8 TRIM2 ABD12 COL11A2 FCO1 TDRD TGFBI CEP1 LTFL1 PRP2 TRPM1 BEST1 COL2A1 GCNT2 CAN TIMM8A CERL MA PRPS1 TTC21B CAPN COLA1 GJA8 FS1 TIMP CM MERT RAB28 TTC8 CRX COLA2 GNPTG TPP1 CIB2 MS RAX2 TLP1 CNJ1 CRAA SF TREX1 CLRN1 MS1 RBP S1C PEX16 CRAB JAG1 TSPAN12 CNGA1 MOA RBP S1G P CRBB1 LRP BIAD1 CNGA NMNAT1 RD S2A RLBP1 CRBB M CNGB1 NPP1 RD12 DR1 OAT CNGB NPP RD RN CNNM NPP RGR NF2

tickler and Cataract ubpanel (4 genes) Genetic testing options for hearing and vision loss (cont’d)

Comprehensive Hearing Loss Panel (92 genes)

ranchio-to-enal elleger yndrome yndrome ubpanel sher yndrome ubpanel (9 genes) (3 genes) ubpanel ( genes)

ACTG1 GF PAX PEX1 EA1 ADGR1 AIFM1 ILDR1 P PEX1 SIX1 CD2 CACNA1D ARS POF PEX1 SIX CIB2 CCDC CN1 POF PEX16 CLRN1 CEACAM16 CN PRPS1 PEX1 ARS CLDN1 LFPL PTPR PEX2 MOA COC LOXD1 RDX PEX PCD1 COL11A2 LRTOMT SERPINB6 PEX6 S1C DFNA MARELD2 SLC26A PEX S1G DFNB MITF SMPX S2A DIABLO MSRB SOX1 RN DIAP1 MT-RNR1 STRC EDN M1 TBC1D2 EDNRB M TECTA ESPN MO1A TIMM8A ESRRB MOA TMC1 EA MO6 TMEM126A GIPC OPA1 TMIE GJB2 OTOA TMPRSS GJB6 OTOF TPRN GPSM2 OTOG TRIOBP GRL2 OTOGL TSPEAR GRXCR1 P2RX2 FS1

Testing can be customized if you would like to order a hearing-specific or vision-specific gene panel. Targeted familial testing is also available. Specimen requirements

Prenatal

Please provide one of the following specimen types: • Two confluent T-25 flasks of cultured cells from amniotic fluid or chorionic villi • >4 mg of direct chorionic villi tissue • 15 mL of direct amniotic fluid 5-10 mL of blood in an EDTA tube (lavender top) is required from each biological parent. Parental blood samples may be used for maternal cell contamination studies or confirmation studies.

Please note: Prenatal analysis will only be performed for known parental variants

Whole blood

Newborn or child • One 2 mL EDTA tube (lavender top) or one 2 mL ACD-A or ACD-B tube (yellow top) from the patient • One 5-10 mL EDTA tube (lavender top) or one 5-10 mL ACD-A or ACD-B tube (yellow top) is also recommended from each biological parent Adult • Two 5-10 mL EDTA tubes (lavender top) or two 5-10 mL ACD-A or ACD-B tubes (yellow top) from the patient • One 5-10 mL EDTA tube (lavender top) or one 5-10 mL ACD-A or ACD-B tube (yellow top) is also recommended from each biological parent

Extracted DNA

• A minimum of 10 µL DNA (50-250 ng/µL) is required for testing. 20 µL DNA (50-350 ng/µL) is recommended

Saliva

• Saliva specimens are accepted upon request. Please contact our laboratory to obtain saliva kits • Saliva samples should be collected in Oragene DNA (OG-500) kits by DNA Genotek Shipping requirements • Tubes of blood, cultured cells, direct chorionic villus sampling, and direct amniotic fluid should be stored and shipped at room temperature or refrigerated. Do not freeze specimens • Please ship specimens same day or overnight to: 1428 Madison Ave, Atran Bldg, Rm 2-25, New York, NY 10029 Turnaround time • Prenatal: 7-10 business days from receipt of specimen • Pediatric or adult: 3-4 weeks from receipt of specimen Advanced genomic technology for highly-accurate results

Next-generation sequencing (NGS) technology is ideal for diagnostic testing of these disorders due to the extreme locus heterogeneity and phenotype overlap of the genes involved. Our customizable targeted NGS panel uses Agilent SureSelect™ target enrichment and Illumina HiSeq sequencing. The sensitivity of this panel is estimated at 99% for single-base substitutions.

If indicated, Sanger sequencing may be performed in both directions using BigDye Terminator chemistry with the ABI 3730 DNA analyzer with target specific amplicons. It may also be used to supplement specific guaranteed target regions that fail NGS sequencing or as a confirmatory method for NGS positive results.

NGS technology may not detect all small insertions or deletions. Additionally, it is not diagnostic for large duplications or deletions, repeat expansions, and structural genomic variation. Therefore, multiplex ligation-dependent probe amplification (MLPA) and oligonucleotide array comparative genomic hybridization (aCGH) are available for this test for deletion/duplication analysis. MLPA copy number analysis is available for the DFNB1 (GJB2/GJB6) locus, OTOA, and STRC. This MLPA testing is approximately 99% accurate. The customized oligonucleotide microarray is a highly-targeted, exon-focused array capable of detecting microdeletions and microduplications at a much higher resolution than traditional aCGH methods. The sensitivity of the aCGH assay is estimated to be greater than 99% for medically-relevant microdeletions and microduplications in the exonic regions of 304 genes.

Please contact 800-298-6470 for additional information or questions about this test.

NGS technology may not detect all small insertions/deletions and is not diagnostic for large duplications/deletions, repeat expansions, and structural genomic variation. This test will only detect variants within the exons and the intron-exon boundaries of the target genes. The following regions were excluded from NGS analysis due to limitations of NGS: ESPN exons 3 and 7, OTOA exons 19 to 27, RP1L1 exon 4, STRC exons 1 to 29, and TRIOBP exon 7. NGS of the MT-RNR1 gene is limited to targeted variant analysis of variants chrM:1494C>T and chrM:1555A>G. aCGH technology cannot detect balanced rearrangements or imbalances that are below the resolution of this array. This technology will also not detect point mutations or small insertion/deletions below this array’s resolution. Copy number variation of MT-RNR1, P2RX2, STRC, and RAB28 will not be reported using aCGH.