Table I.
PECONPI scores from the NSSNHL cohort
This selected PECONPI output focuses on the 35 top-ranking deletion CNVs from 636 NSSNHL probands. The highly ranked large deletions (> 1MB in size) most likely represents undetected syndromic forms of HL including microdeletion syndromes. Rank 3 highlights a homozygous deletion of OTOF. Ranks 23 and 32 include CNTNAP2 deletions. Rank 24 highlights a heterozygous USH2A deletion.
| Rank | Sample ID | Sample Chr | Sample State | Sample Size | Sample #ofSNPs |
Bands | Literature Ovlp% |
Controls# | Total Control Coverage |
Corrected Control Coverage |
Perfect Matches |
Cohort Redundancy |
Genes# | Unique Genes# |
Unique Genes ()=intronic |
Conserved Element # |
Conservation Value |
PECONPI score |
Hyperlink |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HLS407P | Chr6 | hom | 25,868 | 4 | 6q14.1 | 2 | 2 | *MYO6; *SENP6 | 3 | 1000 | 50.7 | link | ||||||
| 2 | HLS372P | Chr9 | het | 4,606,233 | 1,114 | 9q31.1 - q31.2 | 4% | 60 | 8% | 13 | 25 | 24 | *ABCA1; ALDOB; BAAT; C9orf125; CYLC2; FCMD; FSD1L; GRIN3A; MRPL50; *NIPSNAP3A; NIPSNAP3B; OR13C2; OR13C3; OR13C4; OR13C8; OR13C9; OR13D1; OR13F1; PPP3R2; PRG-3; RNF20; SLC44A1; *SMC2; *ZNF189 |
46.6 | link | ||||
| 3 | HLS034P | Chr2 | hom | 21,823 | 5 | 2p23.3 | 1 | 1 | OTOF | 4 | 500 | 45.7 | link | ||||||
| 4 | HLB428 | Chr22 | het | 1,872,299 | 498 | 22q11.21 - q11.23 | 6% | 83 | 19% | 12 | 17 | 14 | BCR; GNAZ; *MAPK1; PPIL2; PPM1F; PRAME; RAB36; RTDR1; SDF2L1; SUHW1; *SUHW2; UBE2L3; VPREB1; *YPEL1 |
45.0 | link | ||||
| 5 | HLS385P | Chr2 | het | 1,045,881 | 70 | 2q11.2 | 44% | 5 | 17 | 17 | ANKRD23; ANKRD36; ANKRD39; ARID5A; ASCC3L1; *CNNM3; CNNM4; FAHD2B; *FLJ10081; *KIAA1641; KIAA1754L; LINCR; LMAN2L; LOC51252; LOC90342; NCAPH; SEMA4C |
44.7 | link | ||||||
| 6 | HLB393 | ChrX | hom | 141,109 | 17 | Xq28 | 3 | 3 | GABRA3; MAGEA10; MAGEA5 | 43.1 | link | ||||||||
| 7 | HLB399 | Chr17 | het | 2,016,861 | 217 | 17q23.2 | 1% | 1 | 12 | 12 | APPBP2; *BCAS3; BRIP1; C17orf64; C17orf82; INTS2; NACAL; PPM1D; TBX2; TBX4; *THRAP1; *USP32 |
42.6 | link | ||||||
| 8 | HLS285 | ChrX | hom | 104,766 | 12 | Xp11.22 | 1 | 1 | PHF8 | 42.2 | link | ||||||||
| 9 | HLS155P | Chr13 | het | 294,448 | 118 | 13q12.11 | 42% | 4 | 2 | 2 | CRYL1; *GJB6 | 1 | 500 | 42.2 | link | ||||
| 9 | HLS170P | Chr13 | het | 294,448 | 118 | 13q12.11 | 42% | 4 | 2 | 2 | CRYL1; *GJB6 | 1 | 500 | 42.2 | link | ||||
| 11 | HLB393 | Chr13 | het | 283,158 | 117 | 13q12.11 | 43% | 4 | 2 | 2 | CRYL1; *GJB6 | 1 | 500 | 42.1 | link | ||||
| 12 | HLB105 | Chr3 | het | 2,694,289 | 397 | 3q13.13 | 6% | 2 | 0% | 8 | 8 | DPPA2; DPPA4; DZIP3; GUCA1C; MORC1; PVRL3; RETNLB; TRAT1 | 42.0 | link | |||||
| 13 | HLB90 | Chr3 | hom | 37,535 | 3 | 3p21.2 | 1 | 2 | 2 | RAD54L2; TEX264 | 41.3 | link | |||||||
| 14 | HLB447 | Chr11 | hom | 27,454 | 4 | 11q13.1 | 2 | 2% | 1 | 1 | 1 | PACS1 | 41.2 | link | |||||
| 15 | HLS123P | Chr2 | hom | 14,084 | 3 | 2p13.1 | 4 | 4 | DOK1; HTRA2; LOC130951; LOXL3 | 40.4 | link | ||||||||
| 16 | HLB122 | ChrX | hom | 2,902 | 4 | Xq28 | 1 | 1 | *TMLHE | 40.4 | link | ||||||||
| 17 | HLS123P | Chr7 | hom | 12,203 | 3 | 7q21.12 | 1 | 1 | *ABCB1 | 40.4 | link | ||||||||
| 18 | HLS403P | Chr3 | hom | 11,533 | 3 | 3q21.1 | 1 | 1 | CCDC14 | 40.4 | link | ||||||||
| 19 | HLS219P | Chr10 | hom | 5,536 | 3 | 10q22.2 | 1 | 1 | SYNPO2L | 40.4 | link | ||||||||
| 20 | HLB421 | ChrX | het | 1,626,888 | 183 | Xp22.31 | 25% | 6 | 17% | 6 | 6 | HDHD1A; PNPLA4; STS; VCX; VCX2; VCX3A | 40.2 | link | |||||
| 21 | HLS489P | Chr4 | het | 548,229 | 177 | 4q35.1 - q35.2 | 2% | 2 | 6 | 6 | CYP4V2; DKFZP564J102; F11; KLKB1; SORBS2; TLR3 | 38.7 | link | ||||||
| 22 | HLB273 | Chr17 | het | 548,740 | 73 | 17q21.31 | 29% | 1 | 5 | 5 | CRHR1; IMP5; KIAA1267; *MAPT; STH | 38.1 | link | ||||||
| 23 | HLS253P | Chr7 | het | 514,993 | 102 | 7q35 | 1 | 1 | 1 | *CNTNAP2 | 37.8 | link | |||||||
| 24 | HLS112P | Chr1 | het | 170,107 | 54 | 1q41 | 1 | 1 | USH2A | 53 | 500 | 37.1 | link | ||||||
| 25 | HLS152P | Chr2 | het | 504,909 | 124 | 2q23.3 | 3% | 1 | 1 | RPRM | 37.0 | link | |||||||
| 26 | HLB167 | Chr3 | het | 472,934 | 83 | 3q25.1 | 6 | 6 | C3orf44; EIF2A; *SELT; *SERP1; SIAH2; TSC22D2 | 36.7 | link | ||||||||
| 27 | HLB451 | Chr14 | het | 432,880 | 86 | 14q21.3 | 21% | 2 | 21% | 1 | 1 | 1 | C14orf155 | 35.9 | link | ||||
| 28 | HLB394 | Chr8 | het | 297,668 | 182 | 8p22 | 69% | 15 | 1% | 2 | 1 | 1 | *TUSC3 | 35.8 | link | ||||
| 29 | HLS154P | Chr22 | het | 507,491 | 143 | 22q11.22 | 71 | 8% | 8% | 10 | 3 | 3 | PRAME; SUHW1; *SUHW2 | 35.8 | link | ||||
| 30 | HLS139P | Chr4 | het | 453,855 | 60 | 4q22.1 | 1 | 1 | MGC48628 | 35.5 | link | ||||||||
| 31 | HLS404P | Chr16 | het | 521,944 | 46 | 16p11.2 | 9% | 27 | 27 | ALDOA; ASPHD1; BOLA2B; C16orf53; C16orf54; CCDC95; CDIPT; *CORO1A; DOC2A; FAM57B; GDPD3; GIYD2; HIRIP3; KCTD13; LOC124446; MAPK3; MAZ; MVP; PPP4C; PRRT2; QPRT; SEZ6L2; SPN; *SULT1A3; TAOK2; TBX6; YPEL3 |
34.8 | link | |||||||
| 32 | HLS087P | Chr7 | het | 281,596 | 63 | 7q35 | 1 | 1 | 1 | *CNTNAP2 | 34.7 | link | |||||||
| 33 | HLB099 | Chr2 | hom | 182,150 | 6 | 2q11.2 | 100% | 4 | 3 | 3 | ANKRD36; FAHD2B; *KIAA1641 | 34.7 | link | ||||||
| 34 | HLS098P | Chr1 | het | 238,644 | 85 | 1q43 | 25% | 1 | 1 | *FMN2 | 34.4 | link | |||||||
| 35 | HLB71 | Chr16 | het | 234,330 | 70 | 16p13.3 | 21% | 2 | 2 | *ADCY9; TFAP4 | 34.3 | link |