Table S1 List of 159 Deafness Genes ACTG1 ADGRV1 ALX3 BSND

BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Med Genet

Table S1 List of 159 deafness genes ACTG1 ADGRV1 ALX3 BSND CABP2 CCDC50 CDH23 CEACAM16 CHD7 CIB2 CLDN14 CLPP CLRN1 COCH COL11A1 COL11A2 COL1A1 COL1A2 COL2A1 COL4A3 COL4A4 COL4A5 COL4A6 COL9A1 COL9A2 CRYM DFNA5 WHRN DFNB59 DIABLO DIAPH1 DIAPH3 DSPP ECM1 EDN3 EDNRB ELMOD3 ESPN ESRRB EYA1 EYA4 FGF3 FGF8 FGFR1 FGFR3 FLNA FOXI1 FREM1 FXN GATA3 GIPC3 GJB1 GJB2 GJB3 GJB6 GLYAT GPSM2 GRHL2 GRXCR1 HARS HARS2 HGF HMX1 HOXA2 HSD17B4 IL13 ILDR1 KARS KCNE1 KCNJ10 KCNQ1 KCNQ4 KITLG KRT9 LAMA3 LARS2 LHFPL5 LOXHD1 LRTOMT MARVELD2 MIR96 MITF MPZ MSRB3 MYH14 MYH9 MYO15A MYO1A MYO1E MYO3A MYO6 MYO7A NDP NDRG1 NEFL NELL2 NF2 OPA1 OTOA OTOF OTOG OTOGL P2RX2 PABPN1 PAX3 PCDH15 PCDH9 PDZD7 PMP22 PNPT1 POLR1C POLR1D POU3F4 POU4F3 PROK2 PROKR2 PRPS1 PTPN11 PTPRQ PTPRR RDX RPGR SALL1 SALL4 SEC23A SEMA3E SERPINB6 SIX1 SIX5 SLC17A8 SLC19A2 SLC26A4 SLC26A5 SMAD4 SMPX SNAI2 SOX10 STRC TBC1D24 TCIRG1 TCOF1 TECTA TIMM8A TJP2 TMC1 TMEM126A TMIE TMPRSS3 TMPRSS4 TNC TPRN TRIOBP TRMU TSPEAR TYR USH1C USH1G USH2A WFS1

Table S2 Six mitochondrial deafness-related regions Locus Location (RefSeq: NC_012920.1) MT-RNR1 chrM:648-1601 MT-TL1 chrM:3230-3304 MT-CO1 chrM:5904-7445 MT-TS1 chrM:7446-7514 MT-TK chrM:8295-8364 MT-TE chrM:14674-14742

Table S3 Three deafness-related miRNAs Name Chromosome Position (hg19) miR-96 chr7: 129414532-129414609 miR-182 chr7: 129410223-129410332 miR-183 chr7: 129414745-129414854

Gao X, et al. J Med Genet 2021; 58:465–474. doi: 10.1136/jmedgenet-2020-106892 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Med Genet

Table S4. Primers of PTPN11 Variants for PCR chromosome Location Variants Forward Primers Reverse Primers chr12-112926851 c.1471C>T GTAGCCATTGCAACATGCTC CCTGCGCTGTAGTGTTTCAA chr12-112888163 c.179G>C CGTTCCTTGGGTTTCTTTCA TTAATTGCCCGTGATGTTCC

chr12-112910827 c.836A>G AATGCTGATCCAGGCTTTTT CCGATGTGCTAACAAGAGCA

chr12-112888172 c.188A>G AAAATCCGACGTGGAAGATG TTCTCTTTTAATTGCCCGTGA

chr12-112891083 c.417G>C TGATCAATCCCTTGGAGGAA TTTAGACTTGCCGTCATTGC chr12-112926851 c.1471G>C GTAGCCATTGCAACATGCTC CCTGCGCTGTAGTGTTTCAA

Table S5 Summary of the candidate variants identified in the NGS test

Nucleotide Amino acid hom/ Allele ACMG code Inheritance Origin of Co-segre Patient ID Gene Transcript change change het Frequency* Pathogenicity mode variant gation PTPN11 NM_002834 c.179G>C p.(Gly60Ala) het - Pathogenic PS1+PS2+ PM2+PP3 AD de novo Yes MYO7A NM_000260 c.3602G>C p.(Cys1201Ser) het 0.004 Likely benign BS2+BP5 AD /AR paternal No 2301 II:1 NDRG1 NM_006096 c.874C>A p.(Leu292Ile) het 0.0008 Likely benign BS2+BP5 AD paternal No SALL1 NM_002968 c.3322G>A p.(Val1108Ile) het 0.0001 Likely benign BS2+BP5 AD paternal No TNC NM_002160 c.2340G>T p.(Glu780Asp) het 0.0001 Likely benign BS2+BP5 AD maternal No PTPN11 NM_002834 c.188A>G p.(Tyr63Cys) het 0.0001 Pathogenic PS1+PS2+ PM2+PP3 AD de novo Yes 2901 II:1 SIX1 NM_005982 c.705G>T p.(Gln235His) het 0.001 Likely benign BS2+BP5 AD maternal No PTPN11 NM_002834.4 c.417G>C p.(Glu139Asp) het - Pathogenic PS1+PS2+ PM2+PP3 AD de novo Yes 6719 II:1 MYO7A NM_000260 c.3602G>C p.(Cys1201Ser) het 0.004 Likely benign BS2+BP5 AD /AR maternal No TECTA NM_005422 c.5488G>A p.(Val1830Met) het 0.004 Likely benign BS2+BP5 AD /AR maternal No PTPN11 NM_002834 c.836A>G p.(Tyr279Cys) het - Pathogenic PS1+PS2+ PM2+PP3 AD de novo Yes DIAPH1 NM_005219 c.2007G>T p.(Leu669Phe het - Likely benign BS2+BP5 AD /AR paternal No 1485 II:1 MYO15A NM_016239 c.7547C>T p.(Ala2516Val) het 0.002 Uncertain significance PM2+BP5 AR maternal Yes MYO15A NM_016239 c.7633G>T p.(Asp2545Tyr) het 0.0005 Uncertain significance PM2+BP5 AR paternal Yes TECTA NM_005422 c.29G>C p.(Trp10Ser) het - Likely benign BS2+BP5 AD /AR maternal No 8728 II:1 PTPN11 NM_002834.4 c.836A>G p.(Tyr279Cys) het - Pathogenic PS1+PS2+ PM2+PP3 AD de novo Yes COL1A1 NM_000088 c.1241C>T p.(Ala414Val) het - Likely benign BS2+BP5 AD /AR paternal No COL9A2 NM_001852 c.1237C>T p.(Pro413Ser) het 0.0002 Likely benign BS2+BP5 AD /AR paternal No DSPP NM_014208 c.1031C>A p.(Thr344Asn) het 0.0002 Likely benign BS2+BP5 AD paternal No PROKR2 NM_144773 c.991G>A p.(Val331Met) het 0.0122 Likely benign BS2+BP5 AD paternal No TBC1D24 NM_001199107 c.1570C>T p.(Arg524Trp) het 0.0033 Likely benign BS2+BP5 AD /AR maternal No PTPN11 NM_002834 c.1471C>G p.(Pro491Ala) het - Likely Pathogenic PS2+ PM2+ PM5+PP3 AD de novo Yes 3001 II:1 TECTA NM_005422 c.4315C>A p.(Leu1439Ile) het 0.0095 Likely benign BS2+BP5 AD /AR paternal No PTPN11 NM_002834 c.1471C>T p.(Pro491Ser) het - Pathogenic PS1+PS2+ PM2+PP3 AD de novo Yes 2442 II:1 GJB2 NM_004004 c.109G>A p.(Val37Ile) het 0.0154 Pathogenic BS2+BP5 AR maternal No 5420 II:1 PTPN11 NM_002834 c.1472C>T p.(Pro491Leu) het - Pathogenic PS1+PS2+ PM2+PP3 AD de novo Yes 1285 II:1 PTPN11 NM_002834 c.1510A>G p.(Met504Val) het - Pathogenic PS1+PS2+ PM2+ PP1+ PP3 AD de novo Yes PTPN11 NM_002834 c.1529A>G p.(Gln510Arg) het - Pathogenic PS1+PS2+ PM2+PP3 AD de novo Yes COL1A1 NM_000088 c.3538C>A p.(Pro1180Thr) het 0.0001 Likely benign BS2+BP5 AD paternal No 1201 II:1 GJB2 NM_004004 c.571T>C p.(Phe191Leu) het 0.0002 Likely benign BS2+BP5 AD /AR paternal No LOXHD1 NM_144612 c.6413G>A p.(Arg2138Gln) het - Uncertain significance PM2+BP5 AR maternal Yes LOXHD1 NM_144612 c.944A>G p.(Lys315Arg) het - Uncertain significance PM2+BP5 AR paternal Yes *: Allele Frequency in East Asian reported by ExAC; -: no data; Bold, back indicates the candidate pathogenic variants; Red indicates compound heterozygous variants with uncertain significance.

Table S6 Summary of PTPN11 variants mosaicism in participants ref/mut Patient ID Variant DNA Source Mutant allele frequency Urine NA c.179G>C 2301 II:1 13444/13802 p.(Gly60Ala) Buccal swab (51%) Urine NA c.188A>G 2901 II:1 37463/34380 p.(Tyr63Cys) Buccal swab (48%) 14383/15003 Urine c.417G>C (51%) 6719 II:1 p.(Glu139Asp) 12063/12400 Buccal swab (51%) 15260/16304 c.836A>G Urine 8728 II:1 (52%) p.(Tyr279Cys) Buccal swab NA 10697/14546 Urine c.1471C>G (58%) 3001 II:1 p.(Pro491Ala) 21148/22087 Buccal swab (51%) 93337/108318 Urine c.1471C>T (54%) 2442 II:1 p.(Pro491Ser) 7615/7274 Buccal swab (49%)

N/A: not available; ref: reference sequence; mut: mutant sequence

Table S7 Average number of hair cells/ supporting cells/ proliferating cells per neuromast in wild-type, morphants and mutant PTPN11 overexpression zebrafish

zebrafish hair cells supporting cells proliferating cells

morphant 2.55 ± 0.998 15.1 ± 2.02 8.0 ± 1.94 Group 1

wild-type 1 7.15 ± 0.988 27.3 ± 2.49 22.6 ± 1.57

mutation 1 5.10±1.197 20.70±3.498 13.50±3.719

Group 2 mutation 2 5.10±1.524 22.30±2.983 13.30±5.579

wild-type 2 7.30±0.949 28.00±5.715 19.70±3.561

The experiments were divided into two groups: group1 (Knockdown group) and group2 (overexpression group). The average number of hair cells, supporting cells and proliferating cells per neuromast in 6 dpf zebrafish were calculated. To determine whether the loss of hair cells and supporting cells was related to decreased cell proliferation, we exposed 4 dpf larvae to BrdU for 48 h

and assessed BrdU incorporation by immunolabeling to visualize cell proliferation.

Figure S1. Loss of ptpn11a causes morphological defects in a dose-dependent manner.

(A) Gross morphology at 5 dpf. Scale bar, 100 μm. (B-C) Quantification of the percentage of embryos

with defects/death.

Figure S2. Quantification data of number and proportion of embryos with development defects

or each phenotype

(A) Raw data of quantitative analysis in Figure 3. (B) Raw data of quantitative analysis in Figure 4. (C)

Raw data of quantitative analysis in Figure 5.

Supplementary experimental methods

DNA preparation

Genomic DNA was extracted from peripheral blood, urine or cells of oral mucosa using the

UniversalGen DNA Kit (ComWin Biotech Co., Ltd. Beijing, China, CW2298) according to the

manufacturer’s instructions.

Data analysis and mosaicism analysis

Following sequencing, Low-quality variations were filtered out using a quality score ≥20 and

Burrows-Wheeler Aligner software (BWA) was used to align the clean reads to the reference human

genome (hg19). Single-nucleotide polymorphisms (SNPs), insertions or deletions (InDels) were

determined using the Genome Analysis Toolkit software (GATK). The candidate sites were screened,

and the reference sequence (ref) and mutation sequence (mut) were counted, then the mutation

frequency was calculated, and the variants mosaic status of different types of samples was evaluated.

Immunostaining

Slides spanning the entire inner ear from C57 mice were stained. For cryosections, the ears of P35

mice were fixed with 4% paraformaldehyde, decalcified, and dehydrated with a graded series of

ethanol. Serial sections were cut at 8-μm thickness. The anti-Shp2 primary antibody (1:100 rabbit

monoclonal antibody; D50F2, #3397S, Cell signaling technology) was used. The primary antibody was

detected with a goat secondary antibody against rabbit conjugated to Alexa Fluor 488 (1:500 Abcam).

Nuclei were labeled with DAPI (1×, ZSJB-Bio, Beijing, China). Negative controls were carried out by

omitting the primary antibody in the first incubation step. For immunostaining of whole-mount cochlea,

mouse cochlea ducts were dissected, fixed, and incubated with anti-Ptpn11 (1:100) and DAPI and

analyzed using a confocal microscope (Leica, TCS SP8, Wetzlar, Germany).

RNA extraction and transcription

Total RNA was extracted from 40 embryos per group using TriPure Isolation Reagent (Roche,

Indianapolis, IN, USA) according to the manufacturer’s instructions. RNA was reverse-transcribed

using the PrimeScript RT reagent Kit with gDNA Eraser (Takara, Otsu, Japan). The primer ef1α

sequences used as the internal control were 5′- GGAAATTCGAGACCAGCAAATAC -3′ (forward)

and 5′- GATACCAGCCTCAAACTCACC -3′ (reverse).

Immunofluorescence staining, cell proliferation assays and quantitative real-time PCR

Larvae (5 dpf MO and wild-type [WT]) were incubated in Embryomedium containing 15 mM

bromodeoxyuridine (BrdU; Sigma Aldrich Canada, Oakville, Ontario, Canada) for 48 h at 28.5°C.

Immunofluorescence staining of neuromasts, cell proliferation assays and quantitative real-time PCR

have been described in detail previously (Gao et al. 2018). Primer sequences are available upon request.

Ten animals for each treatment were quantified and the total signal per animal was averaged. Statistical

analysis and graphical representation of the data were performed using GraphPad Prism 5.0 (GraphPad

Software, San Diego, CA, USA). Statistical significance was performed using Student’s t-test or

analysis of variance where appropriates. Statistical significance is indicated by *P < 0.05, **P<0.01

and ***P < 0.001.

Supplementary references

Gao X, Yuan YY, Lin QF, Xu JC, Wang WQ, Qiao YH, Kang DY, Bai D, Xin F, Huang SS, Qiu SW,

Guan LP, Su Y, Wang GJ, Han MY, Jiang Y, Liu HK, Dai P. Mutation of IFNLR1, an interferon lambda

receptor 1, is associated with autosomal-dominant non-syndromic hearing loss. J Med Genet

2018;55(5):298-306 doi: 10.1136/jmedgenet-2017-104954

jmedgenet-2017-104954 [pii][published Online First: Epub Date]|.

Gao X, et al. J Med Genet 2021; 58:465–474. doi: 10.1136/jmedgenet-2020-106892