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

BMC Medical Genomics

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

	Parameter		SNP 6.0	2.7 M	Omni1	CytoSNP
CNV (standard)	Size		≥50 Kb	≥50 Kb	≥50 Kb	≥50 Kb
CNV (standard)	Marker count^a		≥25	≥25	≥7	≥7
CNV (optimized)	Size	Inside OMIM^b	≥10 Kb	≥10 Kb (loss), ≥50 Kb (gain)	≥10 Kb	≥10 Kb
	Size	Outside OMIM	≥100 Kb	≥200 Kb	≥100 Kb	≥100 Kb
	Marker count	Inside OMIM	≥10	≥10	≥5	≥5
	Marker count	Outside OMIM	≥25	≥25	≥7	≥7
	DGV^c	Outside OMIM	Removed	Removed	N/A	N/A
LCSH	Size		≥5 Mb	≥5 Mb	≥5 Mb	≥5 Mb
LCSH	Marker count		≥100	≥100	≥20	≥20

N/A: non-applicable.
^aAbnormal markers within the CNV or LCSH segment.
^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).
^cCNV completely overlapping with a CNV reported in Database of Genomic Variants (NetAffx Build 30.2).

ISSN: 1755-8794