Table 3. Comparison of DS+AVSD significantly associated CNVs from Sailani and co-workers to our current study using NanoString technology.

	Coordinates (hg19)	Sailani p-Value	Our Cohort p-Value
CNV1
Probe 2	chr21:43,195,101–43,195,176	0.001	0.812
Probe 3	chr21:43,195,664–43,195,743	0.017	0.007
Probe 6	chr21:43,198,103–43,198,173	0.036	0.08
CNV2
Probe 1	chr21:43,411,026–43,411,115	0.014	0.366
Probe 2	chr21:43,411,401–43,411,473	0.018	0.577
Probe 4	chr21:43,412,130–43,412,219	0.001	0.054
Probe 5	chr21:43,412,564–43,412,653	0.004	0.387
Probe 6	chr21:43,412,999–43,413,088	0.016	0.056
Probe 7	chr21:43,413,251–43,413,340	0.008	0.783

We performed NanoString nCounter assays on 46 DS+AVSD cases and 45 DS+NH controls using the same probes used by Sailani et al. (2013) in their CNV replication experiment that included 49 cases and 45 controls. To maintain congruency, we applied their assessment strategy to test for mean differences in normalized count (CN) ratios using a one-sided Mann–Whitney U-test. In CNV1, we detected a significant difference in CN ratios for probe 3 (using Sailani and co-workers’ nomenclature), but did not find this relationship for the other two probes previously found significant by Sailani et al. (2013). In CNV2, two of the six previously significant probes were marginally significant in our experiment. DS+AVSD, individuals with Down syndrome and complete atrioventricular septal defect; DS+NH, individuals with Down syndrome without a congenital heart defect (i.e., normal heart); CNV, copy number variant; chr21, chromosome 21.