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Table 2 Contribution of PCNV/UPD to molecular diagnoses when CMA was performed before, concurrently, or after ES

From: Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases

 

Number of patients

PCNV/UPD by CMA

PCNV/UPD detection rate#

SNV detection rate*

Contribution of PCNV/UPD in molecularly diagnosed cases

ES + CMA

3229

184

5.9% (189/3226)

28.5% (919/3220)

17.4% (189/1089)

CMA done before ES

1977

84

4.6% (91/1977)

32.6% (643/1972)

12.5% (91/727)

 Partially solved

 

63

   

 Inconclusive/non-diagnostic

 

19

   

 Positive only once combined with ES data

 

1

   

 Missed by CMA in original report

 

1

   

Concurrent CMA/ES

1045

75

7.2% (75/1042)

24.1% (251/1041)

23.6% (75/318)

 Solved without ES

 

49

   

 Partially solved

 

22

   

 Inconclusive/non-diagnostic

 

3

   

 Positive only once combined with ES data

 

1

   

CMA done after ES

207

22

11.1% (23/207)

12.1% (25/207)

50.0% (23/46)

 Solved

 

16

   

 Partially solved

 

5

   

 Positive only once combined with ES data

 

1

   
  1. #PCNV/UPD detection rate calculation includes the PCNVs/UPD detected by CMA and/or the QC array
  2. *Does not include cases with autosomal recessive gene deletions or other PCNVs