affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling

Table 2 Results of analyzing Dataset A with aff2sv and MAD

IniProbe	EndProbe	LenProbe	CHR	LRR	Bdev	State	Sample	Pop
219677	33114837	279	8	−0.14	0.088	2	CyHD_022112T_SS199_400554WB	T
43717666	78010194	285	18	0.15	0.07	3	CyHD_022112T_SS199_400554WB	T
20520198	107105043	1140	14	0	0.252	1	N_Blood_control99	N

Mosaic events detected by MAD (T = 7, MinSegLen = 100) on the 627 .CEL files from Afymetrix CytoScan HD corresponding to the two general populations of Nijmegen and Toronto in Dataset A. Each column of the table has its own meaning. IniProbe and EndProbe place the mosaic event on the chromosome given by column CHR. The column LenProbe informs of the number of probes in the region detected as a mosaic event, the columns LRR and Bdev are the measures used to detect the mosaic event and to make a previous attempt to classify it. state shows the result of this classification (being 1 = uniparental disomy (UPD), 2 = Deletion, 3 = Duplication, 4 = Trisomy and 5. = loss of heterozygosity (LOH)). sample tells on which sample the mosaic event was found, and the population on which one of both populations, Toronto (T) or Nijmegen (N), the sample belongs to

ISSN: 1471-2105