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Table 4 Analysis of large low-level mosaic abnormalities in the AGRE autism dataset

From: Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method

Region Sample Chr Size(SNPs) % Mosaic triPOD PSCN MAD BAFseg genoCNA PennCNV
1 AU031003 5 9664 2.1 - 6.4 0.96 0.02 0 0.02 0.06 0
2 AU036104 22 4970 4.9 - 12.6 0.89 0.02 0 0 0 0
3 AU051503 7 7707 3.7 - 10.7 0.69 0.03 0 0 0 0
4 AU068604 5 1499 5.6 - 16.5 1 0 0 0 0 0
5 AU072004 1 19981 6.5 - 18.7 1 0.93 0 0.03 0.05 0
6 AU073006 8 1710 8.4 - 24 0.97 0.87 0.99 0.05 0 0
7 AU0871303 11 5219 2.8 - 8.1 0.99 0 0 0.02 0.03 0
8 AU1271304 9 3202 2.5 – 6.8 0.73 0.39 0 0.01 0.02 0
9 AU1285302 13 7455 7.3 – 21.5 1 1 0.93 1 0.91 0
10 AU1346302 19 3241 6.7 - 19.2 1 0.45 0 0 0 0
11 AU1462303 9 15601 2.2 - 6.0 0.81 0.48 0 0 0 0
12 AU1585303 9 15421 2.8 - 8.1 0.92 0.02 0 0.01 0.07 0
  1. The sensitivity of abnormal region detection for 12 samples in the AGRE autism dataset harboring a large low-level mosaic abnormality is presented. The samples were analyzed by triPOD, BAFsegmentation (unpaired), genoCNA, MAD, PennCNV joint, and PSCN. (Sensitivity results < 0.01 are reported as 0). The % Mosaic column is the estimated percent mosaicism calculated, using BAF values >= the baseline median and < 0.7, as the ratio of the distance of the abnormal BAF median from the baseline median and the expected distance of a 100% mosaic abnormality from the baseline median. For low-level mosaicism, the type of abnormality is difficult to distinguish based on LRR values, thus a range is provided to account for regions resulting from a deletion or UPD event (smaller percentage) or an amplification.