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Table 2 Summary of cell lines and clinical cohorts

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

Panels

IMD_HYB

IMD_PCR

IMD_V1

Batches

3

2

Unknown

Samples

30a (cell line)

36 (clinical)

14 (cell line)

20 (clinical)

178 (clinical)

Average depth of coverage

174X

345X

301X

349X

87X

Samples passing QC

24

35

14

19

172

Failure rate

20%

2.8%

0%

5%

3.4%

Median number of raw duplications

52.5

8

35.5

29

22.5

Median number of raw deletions

22.5

3

37

23

9

Median number of raw CNVs

82

13

85.5

67

34.5

Median number of 5-scoreb duplications

4.5

1

12

5

6

Median number of 5-score deletions

2

0

5.5

2

1

Median number of 5-score CNVs

6.5

1

24.5

7

7.5

  1. QC quality control, CNV copy number variation, IMD inherited metabolism disorder, HYB hybridization-based capture approach, PCR polymerase chain reaction-based capture approach
  2. a27 unique cell line. Total 30 samples were sequenced because two cell lines were generated 3 times respectively
  3. bHigh-confidence CNVs received the highest score of 5