Genomic analysis of Notch mutations in a case of Alagille Syndrome with Acute Lymphoblastic
Genomic DNA was quantified using the Quant-iT PicoGreen dsDNA Assay Kit on a NanoDrop 3300 fluorospectrometer. Then, 1.3 μg of DNA was sheared to 100-450 bp on a Covaris S220 instrument. Fragmentation was verified on the Agilent 2100 Bioanalyzer using a DNA 1000 assay. Sheared DNA was subjected to Illumina  paired-end DNA library preparation using the TruSeq DNA Sample preparation kit. The quality of the library was evaluated with an Agilent High Sensitivity DNA assay and then quantified using the Quant-iT PicoGreen dsDNA Assay Kit on a NanoDrop 3300 fluorospectrometer. Exome capture was performed starting from 500 ng of  library as input material with TruSeq Exome Enrichment Kit following manufacturer instruction. The quality of the whole exome library was checked with an Agilent High Sensitivity DNA assay and quantified by qPCR on a Stratagene MX3000P using Kapa Library Quant kit. Whole exome library was sequenced with an Illumina HiSeq 1000 sequencer and 100-bp paired-end sequences were generated.