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Table 6 Candidate pathogenic CNVs detected by clinical sample analysis using DeviCNV

From: DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data

Sample

CNV candidates after scoringa

Selected pathogenic CNVsc

Panel

Sample

Median

read depth

Raw CNVb

Score 5

Score 4

Score 3

Score 2

Score 1

Score 0

Gene

NM

CNV

CNV size (kb)

Confirmed by qPCR

IMD_HYB

Case_01

273.3

49

2

22

20

5

0

0

ACADVL

NM_000018

EX2 DEL (Score 4)

0.08

Failed

Case_02

341.4

12

7

3

2

0

0

0

ASL

NM_000048

EX15 DEL (Score 5)

0.08

Confirmed

Case_03

276.8

25

5

18

2

0

0

0

GYS2

NM_021957

EX6–11 DEL (Score 5)

5.15

Partially confirmed (EX6–7, 10–11)

IMD_PCR

Case_04

Pool 1: 174.0 Pool 2: 203.0 Pool 3: 185.0

82

26

46

9

1

0

0

ETFDH

NM_004453

EX1–7 DEL (Score 5)

23.51

Confirmed

Case_05

Pool 1: 228.0 Pool 2: 330.0 Pool 3: 185.0

145

63

74

8

0

0

0

ETFDH

NM_004453

EX7–8 DEL (Score 5)

2.20

Confirmed

IMD_V1

Case_06

Pool 1: 69.0 Pool 2: 56.0

106

37

40

26

3

0

0

OTC

NM_000531

EX2 DEL (Score 5)

0.14

Confirmed

Case_07

Pool 1: 52.0 Pool 2: 51.0

65

23

23

14

5

0

0

OTC

NM_000531

Entire gene DEL (Score 5)

68.38

Confirmed

  1. CNV copy number variation, IMD inherited metabolism disorder; HYB hybridization-based capture approach, PCR polymerase chain reaction-based capture approach, EX exon, DEL deletion, DUP duplication, qPCR quantitative polymerase chain reaction
  2. aIndicates the number of CNV candidates for each score
  3. bindicates the number of all CNV candidates before scoring
  4. cindicates the selected pathogenic CNVs identified in the clinical sample by one expert. The number in parentheses indicates the score of the selected CNV