Exploring the genetic landscape of auditory function

Genetics of hearing loss In man, ~150 loci have been identified ~88 DFNB (recessive) ~59 DFNA (dominant) 6 DFNX (X-linked) ~ 103 causative genes have been identified Two-thirds of genes are for DFNB forms Diverse function Safieddine et al, Annu.Rev. Neurosci, 2012

The International Mouse Phenotyping Consortium (IMPC) Building the first comprehensive functional catalogue of a mammalian genome www.mousephenotype.org

IMPC phenotyping pipeline Embryonic Adult ABR 2 males + 2 females Click + 6, 12, 18, 24, 30kHz

Identification of ABR phenodeviants Reference Range Plus was employed using the ‘testDataset’ function within PhenStat 1. A reference range was created from matched wild type data 2.5% 97.5% Wildtype data Sorted wildtype data 95% reference range 2. The numbers of animals that were higher than the range from the wildtype and mutant values were tabulated into a contingency table Within range Higher than range Wild type 82 2 Mutant 3. A Fisher’s Exact Test was then performed to determine the probability that both groups (wild type and mutant) were from the same distribution For the above example table: p=0.00164

3006 IMPC genotypes A suitable reference range and critical p value for the Fisher’s determined by expert examination of the lists of putative phenodeviants using different critical values Known deafness genes were employed to aid critical value selection A 98% reference range, and a 0.01 critical p value were initially selected. 328 candidates were manually curated to produce a definitive list of phenodeviants This provided a curated list of 67 phenodeviant lines 328 Candidate phenodeviants 67 curated phenodeviants

Manual Curation Lines showing discordant thresholds within, and between, genders were removed Lines that exhibited elevated thresholds at only one of their middle-range frequencies (12, 18 or 24 kHz) were removed This led to 261 lines being eliminated from further analysis Lines that showed highly concordant elevated thresholds at either, low frequency (6 kHz), high frequency (30 kHz), or across two or more frequencies, were deemed to be true hearing loss mutants (65 lines) Lines with hearing thresholds that were discordant between gender, but concordant within gender were also deemed to be true hearing loss mutants (2 lines)

Manual Curation Only 9 of 261 genes excluded have some association with a deafness phenotype

ABR Thresholds Deafness mutations identified from IMPC centres around the globe

Deafness types Severe Deafness at all frequencies (25 genes): A730017C20Rik, Adgrv1, Cib2, Clrn1, Col9a2, Duoxa2, Elmod1, Eps8l1, Gipc3, Ildr1, Klc2, Marveld2, Myo7a, Nedd4l, Nptn, Ocm, Otoa, Slc5a5, Spns2, Tmem30b, Tmtc4, Tox, Tprn, Ush1c, Zfp719 Mild Deafness at all frequencies (19 genes): Acvr2a, Adgrb1, Ankrd11, Ap3m2, Ap3s1, Baiap2l2, Ccdc92, Cyb5r2, Gga1, Mpdz, Myh1, Nisch, Odf3l2, Slc4a10, Srrm4, Tram2, Ube2b, Ube2g1, Vti1a

Deafness types Deafness at High frequencies (13 genes): Aak1, Acsl4, Ahsg, Ccdc88c, Dnase1, Emb, Ewsr1, Gpr152, Ikzf5, Nin, Phf6, Ppm1a, Wdtc1 Deafness at Low frequencies (10 genes): Atp2b1, B020004J07Rik, Gata2, Gpr50, Il1r2, Klhl18, Med28, Nfatc3, Sema3f, Zcchc14

Severe Deafness at all frequencies Severe Deafness at all frequencies (25 genes): A730017C20Rik, Adgrv1, Cib2, Clrn1, Col9a2, Duoxa2, Elmod1, Eps8l1, Gipc3, Ildr1, Klc2, Marveld2, Myo7a, Nedd4l, Nptn, Ocm, Otoa, Slc5a5, Spns2, Tmem30b, Tmtc4, Tox, Tprn, Ush1c, Zfp719

Severe Deafness at all frequencies Severe Deafness at all frequencies (25 genes): A730017C20Rik, Adgrv1, Cib2, Clrn1, Col9a2, Duoxa2, Elmod1, Eps8l1, Gipc3, Ildr1, Klc2, Marveld2, Myo7a, Nedd4l, Nptn, Ocm, Otoa, Slc5a5, Spns2, Tmem30b, Tmtc4, Tox, Tprn, Ush1c, Zfp719

Severe Deafness at all frequencies Severe Deafness at all frequencies (25 genes): A730017C20Rik, Adgrv1, Cib2, Clrn1, Col9a2, Duoxa2, Elmod1, Eps8l1, Gipc3, Ildr1, Klc2, Marveld2, Myo7a, Nedd4l, Nptn, Ocm, Otoa, Slc5a5, Spns2, Tmem30b, Tmtc4, Tox, Tprn, Ush1c, Zfp719

Severe Deafness at all frequencies Severe Deafness at all frequencies (25 genes): A730017C20Rik, Adgrv1, Cib2, Clrn1, Col9a2, Duoxa2, Elmod1, Eps8l1, Gipc3, Ildr1, Klc2, Marveld2, Myo7a, Nedd4l, Nptn, Ocm, Otoa, Slc5a5, Spns2, Tmem30b, Tmtc4, Tox, Tprn, Ush1c, Zfp719

Severe Deafness at all frequencies Nedd4l, neural precursor cell expressed, developmentally down-regulated gene 4-like Nptn, neuroplastin Severe Deafness at all frequencies (25 genes): A730017C20Rik, Adgrv1, Cib2, Clrn1, Col9a2, Duoxa2, Elmod1, Eps8l1, Gipc3, Ildr1, Klc2, Marveld2, Myo7a, Nedd4l, Nptn, Ocm, Otoa, Slc5a5, Spns2, Tmem30b, Tmtc4, Tox, Tprn, Ush1c, Zfp719

Mild Deafness at all frequencies Mild Deafness at all frequencies (19 genes): Acvr2a, Adgrb1, Ankrd11, Ap3m2, Ap3s1, Baiap2l2, Ccdc92, Cyb5r2, Gga1, Mpdz, Myh1, Nisch, Odf3l2, Slc4a10, Srrm4, Tram2, Ube2b, Ube2g1, Vti1a

Mild Deafness at all frequencies Mild Deafness at all frequencies (19 genes): Acvr2a, Adgrb1, Ankrd11, Ap3m2, Ap3s1, Baiap2l2, Ccdc92, Cyb5r2, Gga1, Mpdz, Myh1, Nisch, Odf3l2, Slc4a10, Srrm4, Tram2, Ube2b, Ube2g1, Vti1a

Mild Deafness at all frequencies Tram2, translocating chain-associating membrane protein 2 Mild Deafness at all frequencies (19 genes): Acvr2a, Adgrb1, Ankrd11, Ap3m2, Ap3s1, Baiap2l2, Ccdc92, Cyb5r2, Gga1, Mpdz, Myh1, Nisch, Odf3l2, Slc4a10, Srrm4, Tram2, Ube2b, Ube2g1, Vti1a

Deafness at High frequencies Deafness at High frequencies (13 genes): Aak1, Acsl4, Ahsg, Ccdc88c, Dnase1, Emb, Ewsr1, Gpr152, Ikzf5, Nin, Phf6, Ppm1a, Wdtc1

Deafness at High frequencies Deafness at High frequencies (13 genes): Aak1, Acsl4, Ahsg, Ccdc88c, Dnase1, Emb, Ewsr1, Gpr152, Ikzf5, Nin, Phf6, Ppm1a, Wdtc1

Deafness at High frequencies Emb, Embigin Wdtc1, WD and tetratricopeptide repeats 1 Deafness at High frequencies (13 genes): Aak1, Acsl4, Ahsg, Ccdc88c, Dnase1, Emb, Ewsr1, Gpr152, Ikzf5, Nin, Phf6, Ppm1a, Wdtc1

Deafness at Low frequencies Deafness at Low frequencies (10 genes): Atp2b1, B020004J07Rik, Gata2, Gpr50, Il1r2, Klhl18, Med28, Nfatc3, Sema3f, Zcchc14

Deafness at Low frequencies Deafness at Low frequencies (10 genes): Atp2b1, B020004J07Rik, Gata2, Gpr50, Il1r2, Klhl18, Med28, Nfatc3, Sema3f, Zcchc14

Deafness at Low frequencies Atp2b1, ATPase, Ca++ transporting, plasma membrane 1 Sema3f, semaphorin 3F Deafness at Low frequencies (10 genes): Atp2b1, B020004J07Rik, Gata2, Gpr50, Il1r2, Klhl18, Med28, Nfatc3, Sema3f, Zcchc14

Neuroplastin (Nptn) and Embigin (Emb)

Summary – novel deafness genes - from 3006 lines analysed by ABR A730017C20Rik Aak1 Acsl4 Acvr2a Adgrb1 Ahsg Ankrd11 Ap3m2 Ap3s1 Ap4e1 Atg4b Atp2b1 B020004J07Rik Baiap2l2 Ccdc88c Ccdc92 Cyb5r2 Dnase1 Duoax2 Emb Eps8l1 Ewsr1 Gga1 Gpr152 Gpr50 Ikzf5 Il1r2 Klc2 Klhl18 Med28 Mpdz Myh1 Nedd4l Nfatc3 Nin Nisch Nptn Odf3l2 Phf6 Ppm1a Sema3f Slc4a10 Slc5a5 Spsn2 Tmem30b Tmtc4 Tox Tram2 Ube2b Ube2g1 Vti1a Wdtc1 Zcchc14 Zfp719 67 Known Deafness Genes Novel Deafness Genes Known Genes Adgrv1 Clrn1 Elmod1 Gata2 Gipc3 Ildr1 Marveld2 Myo7a Ocm Otoa Srrm4 Tprn Ush1c 15 52 Known Genes with mouse mutations for the first time 13 2 Novel Genes Cib2 Col9a2

Network interaction map incorporating known and novel deafness genes DFNA DFNA/DFNB IMPC NOVEL IMPC KNOWN DFNB DFNX 65 known deafness genes from a core hub, including 11 novel IMPC genes 41 novel genes were unconnected, free nodes

Conclusions IMPC has revealed a large number of novel deafness genes underlying a variety of types of hearing loss 67 genes identified from 3000 loci analysed would suggest a minimum of 450 deafness genes Taking into account genes involved with progressive and late onset hearing loss, we can expect the number of deafness genes to rise further From the 100 lines being phenotyped every month by IMPC, we can expect around 2 novel deafness genes – around 25 new deafness genes every year

MRC Harwell Institute Mike Bowl Michelle Simon Simon Greenaway Luis Santos