TABLE 1.
Twenty-four CNCs identified by both XHMM and CoNIFER and present in more than one NSCLP patient.
| Gene | Event type |
Length (kb) |
Chromosome | Start/End coordinates* |
Families | qPCR testing |
Pedigree analysis** |
CoNIFER Scores*** |
XHMM Scores*** |
|---|---|---|---|---|---|---|---|---|---|
| ODF2L | Deletion | 4.79 | 1 | 86847923 – 86852712 | M28 | TRUE | Does not segregate | ||
| KIFAP3 | Deletion | 56.42, 60.35 | 1 | 169947224 – 170003639 169947224 – 170007574 | M45, M94 | FALSE | |||
| HOOK1 | Deletion | 2.14, 8.89 | 1 | 60305970 – 60314857 60312716 – 60314857 | M45 | FALSE | |||
| CRYZ | Deletion | 10.27 | 1 | 75180237 – 75190507 | M1 | TRUE | Segregates | −1.71 – −1.64 | −7.0 – −7.4 |
| WDPCP | Deletion | 50.1 | 2 | 63664553 – 63714656 | M55, M62 | FALSE | |||
| APLF | Deletion | 10.95 | 2 | 68729861 – 68740814 | M28, M62 | FALSE | |||
| FSIP2**** | Deletion | 8.82 | 2 | 186397377 – 186406199 | M55, M62 | TRUE | Does not segregate | ||
| ARPP21 | Deletion | 9.26 | 3 | 35723242 – 35732499 | M28, M62 | TRUE | Does not segregate | ||
| CACNA1D | Duplication | 226.17 | 3 | 53699685 – 53925858 | M71 | TRUE | Does not segregate | ||
| ADH7 | Duplication | 7.69 | 4 | 100334266 – 100341952 | M1 | TRUE | Segregates | 1.72 | 4.56 – 5.93 |
| ZNF608 | Duplication | 11.85 | 5 | 123973545 – 123985398 | M55 | TRUE | Does not segregate | ||
| WDR36 | Deletion | 6.86, 9.38, 20.56 | 5 | 110436286 – 110443138 110436286 – 110456839 110439483 – 110448852 | M28, M45, M46 | TRUE | Does not segregate | ||
| UFL1 | Deletion | 14.15, 14.56, 15.69, 19.27 | 6 | 96982117 – 97001381 96985248 – 96999808 96985248 – 96999401 96984118 – 96999808 | M17, M28, M55, M62 | FALSE | |||
| TRDN | Deletion | 31.02, 33.88 | 6 | 123539745 – 123573621 123542598 – 123573621 | M28, M62 | FALSE | |||
| NKAIN2 | Duplication | 165.09 | 6 | 124979330 – 125144422 | M46 | TRUE | Does not segregate | ||
| CACNA2D1 | Deletion | 4.74, 10.53 | 7 | 81593347 – 81603871 81596453 – 81601188 | M45, M62 | TRUE | Does not segregate | ||
| AHR | Deletion | 13.3, 23.6 | 7 | 17349559 – 17843203 17362123 – 17841282 17367382 – 17841282 | M45 | TRUE | Segregates | −0.735 – −0.517 | −2.76 |
| DDX18**** | Deletion | 133.09 | 9 | 118289457 – 118422544 | M28, M62 | TRUE | Does not segregate | ||
| DHTKD1 | Duplication | 36.35, 39.42, 51.86 | 10 | 12123469 – 12162889 12126537 – 12162889 12111031 – 12162889 | M16, M67 | TRUE | Does not segregate | ||
| FAM76B | Deletion | 8.4, 11.71 | 11 | 95504718 – 95513118 95504718 – 95516430 | M28, M45 | FALSE | |||
| PCNX | Duplication | 147.71 | 14 | 71428941 – 71576654 | M94 | TRUE | Does not segregate | ||
| VPS13C | Deletion | 32.2, 35.63 | 15 | 62304283 – 62336484 62300852 – 62336484 | M28, M45 | TRUE | Does not segregate | ||
| CGNL1 | Duplication | 23.9 | 15 | 57730196 – 57754092 | M53, M71 | TRUE | Does not segregate | ||
| C18orf54 | Deletion | 8.59, 11.53 | 18 | 57730196 – 57754092 | M28, M45 | TRUE | Does not segregate |
The CNC details and families in which they were called are listed.
*
Start and end coordinates from XHMM are listed.
**
Segregation of a CNC with NSCLP is defined as presence of the CNC in all family members affected by NSCLP within a family.
***
The CoNIFER score represents the median signal strength of the calls (median_svdzrpkm). The XHMM score shows the mean normalized read depth z-scores over the interval.
****
For CNC calls corresponding to intergenic regions, the gene for the closest exon is listed.