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.

ABCA4ABHD12ADAM9AGKAHI1AIPL1ALMS1AP3B1ARL13BARL6BBS1BBS10BBS12BBS2BBS4BBS5BBS7BBS9BCORBEST1BLOC1S6BMP4C2orf71C5orf42C8orf37CA4CABP4CACNA1FCACNA2D4CAPN5CC2D2ACDH3CDHR1CEP164CEP290CEP41CERKLCHMCLN3CLN5CLN6CLN8CNGA1CNGA3

CNGB1CNGB3CNNM4COL11A1COL2A1COL9A1COL9A2CRB1CRXCRYAACRYABCRYBB1CRYBB3CTSDCYP1B1CYP4V2DHDDSDNAJC5EFEMP1ELOVL4ERCC6EYSFAM161AFLVCR1FOXC1FOXE3FRAS1FREM1FREM2FRMD7FSCN2FYCO1FZD4GCNT2GJA8GNAT1GNAT2GNPTGGPR143GPR179GRIP1GRK1GRM6GUCA1A

GUCA1BGUCY2DHCCSHESX1HPS1HPS3HPS4HPS5HPS6HSF4IFT140IMPDH1IMPG2INPP5EIQCB1JAG1KCNJ13KCNV2KIF11KIF7KLHL7LCA5LRATLRIT3LRP5LYSTLZTFL1MAKMERTKMFRPMFSD8MKKSMKS1MTTPMYOCNDPNMNAT1NPHP1NPHP3NPHP4NR2E3NRLNYXOAT

OCA2OFD1OPA3OPN1SWOTX2PANK2PAX6PDE6APDE6BPDE6CPDE6GPDE6HPGK1PITPNM3PITX2PITX3PLA2G5PPT1PRCDPROM1PRPF3PRPF31PRPF6PRPF8PRPH2PXDNRAB28RAX2RBP3RBP4RD3RDH12RDH5RGRRGS9RGS9BPRHORIMS1RLBP1ROM1RP1RP1L1RP2RPE65

RPGRRPGRIP1RPGRIP1LRS1SAGSDCCAG8SEMA4ASLC24A1SLC45A2SMOC1SNRNP200SOX2SPATA7STRA6TCTN1TCTN2TCTN3TDRD7TGFBITIMP3TMEM216TMEM231TMEM237TMEM67TOPORSTPP1TREX1TRIM32TRPM1TSPAN12TTC21BTTC8TULP1TYRTYRP1UBIAD1VCANVSX2WDR19ZNF423

ADGRV1CDH23CIB2CLRN1COL11A2EDN3EDNRBEYA1HARSMITFMYH9MYO7AOPA1PAX3PCDH15PEX1PEX10PEX14PEX16PEX19PEX2PEX5PEX6PEX7PHYHPRPS1SOX10TIMM8ATMEM126AUSH1CUSH1GUSH2AWFS1WHRN

Comprehensive Vision Loss Panel (250 genes)Comprehensive Hearing

Loss Panel (92 genes)

ACTG1AIFM1CACNA1DCCDC50CEACAM16CLDN14COCHDFNA5DFNB59DIABLODIAPH1ESPNESRRBEYA4GIPC3GJB2GJB6GPSM2GRHL2GRXCR1HGFILDR1KARSKCNQ1KCNQ4LHFPL5LOXHD1LRTOMTMARVELD2MSRB3MT-RNR1MYH14

MYO15AMYO3AMYO6OTOAOTOFOTOGOTOGLP2RX2POU3F4POU4F3PTPRQRDXSERPINB6SIX1SIX5SLC26A4SMPXSTRCTBC1D24TECTATMC1TMIETMPRSS3TPRNTRIOBPTSPEAR

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)

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)

CRB1CYP4V2DHDD2EYSFAM161AFLVCR1FSCN2GNAT2GPR179GRK1GRM6GUCA1AGUCA1BGUCY2DHARSIFT140IMPDH1IMPG2INPP5EIQCB1KCNV2KIF7KLHL7LCA5LRATLRIT3LZTFL1MAKMERTKMKKSMKS1MYO7ANMNAT1NPHP1NPHP3NPHP4

Retinal Disease Subpanel (154 genes)

De

velo

pm

en

tal E

ye

Su

bp

an

el (21 g

en

es)

Albinism, Hermansky-Pudlak Syndrome, and Waardenburg Syndrome Subpanel (18 genes)

Stickler and Cataract Subpanel (41 genes)

CABP4CDH3CLN3CLN5CLN6CLN8CTSDCYP1B1DNAJC5EFEMP1ELOVL4 FRMD7 FZD4 GNAT1 HESX1 LYST MFSD8 MTTP MYOC NYX PGK1 PITX2PPT1RGS9RGS9BPRS1TGFBITIMM8ATIMP3TPP1TREX1TSPAN12UBIAD1

ABCA4ADAM9ADGRV1AHI1AIPL1ALMS1ARL13BARL6BBS1BBS10BBS12BBS2BBS4BBS5BBS7BBS9C2orf71C5orf42C8orf37CA4CACNA2D4CC2D2ACDH23CDHR1CEP164CEP290CEP41CERKLCHMCIB2CLRN1CNGA1CNGA3CNGB1CNGB3CNNM4

NR2E3NRLOFD1OPA1OPN1SWPANK2PCDH15PDE6APDE6BPDE6CPDE6GPDE6HPEX1PEX10PEX14PEX19PEX2PEX5PEX6PITPNM3PRCDPROM1PRPF3PRPF31PRPF6PRPF8PRPH2PRPS1RAB28RAX2RBP3RBP4RD3RDH12RDH5RGR

RHORIMS1ROM1RP1RP1L1RP2RPE65RPGRRPGRIP1RPGRIP1LSAGSDCCAG8SEMA4ASLC24A1SNRNP200SPATA7TCTN1TCTN2TCTN3TMEM126ATMEM216TMEM231TMEM237TMEM67TOPORSTRIM32TRPM1TTC21BTTC8TULP1USH1CUSH1GUSH2AWDR19WHRNZNF423

CACNA1F

AP3B1BLOC1S6EDN3EDNRBGPR143HPS1

HPS3HPS4HPS5HPS6MITFOCA2

PAX3SLC45A2SOX10TYRTYRP1

BMP4FOXC1FOXE3FRAS1FREM1

FREM2GRIP1HCCSK1F11

PLA2G5SMOC1SOX2STRA6

PAX6PITX3PXDN

VSX2BCORNDPOTX2

AGKCOL11A1COL11A2COL2A1COL9A1COL9A2CRYAACRYABCRYBB1CRYBB3

ERCC6EYA1FYCO1GCNT2GJA8GNPTGHSF4JAG1LRP5MYH9OAT

OPA3PEX7TDRD7VCANWFS1

MFRP

ABHD12BEST1CAPN5CRXKCNJ13PEX16PHYHRLBP1

Zellweger Syndrome Subpanel (9 genes)

Branchio-Oto-Renal Syndrome Subpanel

(3 genes)Usher Syndrome

Subpanel (11 genes)

PEX1PEX10PEX14PEX16PEX19PEX2PEX5PEX6PEX7

ACTG1AIFM1CACNA1DCCDC50CEACAM16CLDN14COCHCOL11A2DFNA5DFNB59DIABLODIAPH1EDN3EDNRBESPNESRRBEYA4GIPC3GJB2GJB6GPSM2GRHL2GRXCR1

HGFILDR1KARSKCNQ1KCNQ4LHFPL5LOXHD1LRTOMTMARVELD2MITFMSRB3MT-RNR1MYH14MYH9MYO15AMYO3AMYO6OPA1OTOAOTOFOTOGOTOGLP2RX2

PAX3PHYHPOU3F4POU4F3PRPS1PTPRQRDXSERPINB6SLC26A4SMPXSOX10STRCTBC1D24TECTATIMM8ATMC1TMEM126ATMIETMPRSS3TPRNTRIOBPTSPEARWFS1

EYA1SIX1SIX5

ADGRV1CDH23CIB2CLRN1HARSMYO7APCDH15USH1CUSH1GUSH2AWHRN

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

Comprehensive Hearing Loss Panel (92 genes)

Genetic testing options for hearing and vision loss (cont’d)

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

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.

© 2018 Mount Sinai Genomics, Inc. D/B/A Sema4. All rights reserved. LLP0204GE0418sema4.com

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

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.

Advanced genomic technology for highly-accurate results