1. Exploring the genetic landscape of auditory function

2. 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

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

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

5. 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=

6. 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

7. 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)

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

9. ABR Thresholds
Deafness mutations identified from IMPC centres around the globe

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

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

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

22. 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

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

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

25. 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

26. Neuroplastin (Nptn) and Embigin (Emb)

27. 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

28. 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

29. 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

30. MRC Harwell Institute Mike Bowl Michelle Simon Simon Greenaway
Luis Santos