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Table 2 ChAS and KaryoStudio thresholds used for CNV and LCSH visualization

From: SNP arrays: comparing diagnostic yields for four platforms in children with developmental delay

  Parameter SNP 6.0 2.7 M Omni1 CytoSNP
CNV (standard) Size   ≥50 Kb ≥50 Kb ≥50 Kb ≥50 Kb
Marker counta   ≥25 ≥25 ≥7 ≥7
CNV (optimized) Size Inside OMIMb ≥10 Kb ≥10 Kb (loss),
≥50 Kb (gain)
≥10 Kb ≥10 Kb
Outside OMIM ≥100 Kb ≥200 Kb ≥100 Kb ≥100 Kb
Marker count Inside OMIM ≥10 ≥10 ≥5 ≥5
Outside OMIM ≥25 ≥25 ≥7 ≥7
DGVc Outside OMIM Removed Removed N/A N/A
LCSH Size   ≥5 Mb ≥5 Mb ≥5 Mb ≥5 Mb
Marker count   ≥100 ≥100 ≥20 ≥20
  1. N/A: non-applicable.
  2. aAbnormal markers within the CNV or LCSH segment.
  3. b OMIM : Regions containing genes of known clinical relevance from the NCBI Online Mendelian Inheritance in Man Morbid Map (February 2009 hg19 assembly, accessed October 28, 2010).
  4. cCNV completely overlapping with a CNV reported in Database of Genomic Variants (NetAffx Build 30.2).