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Table 1 Recommendations concerning the detection and reporting criteria for diagnostic array results and follow-up testing

From: Best diagnostic approach for the genetic evaluation of fetuses after intrauterine death in first, second or third trimester: QF-PCR, karyotyping and/or genome wide SNP array analysis

Detection criteria

Gain

Loss

ROH

 

Minimum marker count

10

10

500 (SNP probes)

 

Minimum size (kb)

20

10

1250

 

Reporting criteria

Gene content of CNV

Size of CNV (kb)

  
 

Known disease gene, matching the phenotype

<20

  
 

Known disease gene(s)*

>20

  
 

No disease gene(s)

>100

  
 

No genes

>500

  
 

ROH

Size of ROH (Mb)

  
  

> 10

Genomic Oligoarray and SNP array evaluation tool v2.0 [24] → recessive disease causing genes → mutation detection

Positive → Parental mutation carrier analysis

  

< 10

In case of a specific clinical suspicion for a known syndrome → Genomic Oligoarray and SNP array evaluation tool v2.0 [24] →recessive disease causing genes → mutation detection

Positive → Parental mutation carrier analysis

Parental testing

Type of CNV

Follow-up test

  
 

Uncertain

Array analysis

  
 

Clinically relevant:

   
 

- cytogenetically visible (> 5–10 Mb)

Karyotyping

  
 

- submicroscopic aberration (<1-10 Mb)

FISH

  
  1. *Depending on the referral reason for array, in this case intrauterine fetal death, a certain CNV will sometimes not be reported, even though our general reporting criteria are met. For example, if it concerns a 50 kb loss in an OMIM disease gene that is not involved in embryonic and fetal development. Alternatively, a certain CNV is reported, but in the explanatory text of the array report it is mentioned that this CNV is not very likely causative for the IUFD.