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[null,"Table S1: Heterogeneity of strategies for dealing with copy number variable regions in allele-specific mapping analyses in twelve studies"]
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[null,"Study","Tool","ASE/ASB","Integrative analysis of multiple samples","Samples","Statistical Method","Strategy to deal with copy number data","Input file requirments"]
[null,"McDaniell et al., 2010","--","ASB","No","lymphoblastoid cell lines (LCLs) derived from two parent-offspring trios","Binomial test (> 15 reads)","None","--"]
[null,"Rosowsky et al., 2011","AlleleSeq","Both","No"," GM12878 (ENCODE)","Binomial test","Filter out heterozygous sites if they lie in regions predicted to be copy number variants as determined by the read depth of the genome sequencing data","1. Fasta files of reference genome and user input reads. 2. SNV and CNV  3. RF binding sites (optional)"]
[null,"Li Gand et al., 2012","--","ASE","No","Glioblastoma cell line U87MG and primary breast cancer tissues","Chi-square test ( > 20 reads)","Filter out heterozygous sites if they lie in regions predicted to be copy number variants as determined by the read depth of the genome sequencing data","--"]
[null,"Reddy et al., 2012","--","ASB","No"," GM12878 (ENCODE)","Binomial test (> 7 reads)","Remove variants with allelic bias in the input control DNA; Removed 10 (<0.05% of total) heterozygous sites that overlapped regions of aneuploidy as measured by microarray experiments","--"]
[null,"Wei et al., 2012","iASeq","ASB","Yes","GM12878 (ENCODE)","Beta-binomial model","None","Read counts for both alleles. "]
[null,"Kasowski et al., 2013","--","Both","No","Lymphoblastoid cell lines (LCLs) derived from 19 individuals (1K Genomes project)","Binomial","None","--"]
[null,"Kilpinen et al., 2013","--","Both","No","lymphoblastoid cell lines (LCLs) derived from two parent-offspring trios","Binomial (>10-20 reads) ","None","--"]
[null,"Almlöf et al., 2014","--","ASE","No","Human monocytes purified from white blood cells of 188 healthy blood donors","None","ASE levels were calculated as the difference in normalized allele fractions between cDNA and gDNA","--"]
[null,"Mayba et al., 2014","MBASED","ASE","No","Human lung cancer cell lines and paired tumor-normal lung and liver tissue samples","Beta-binomial model (> 10 reads)","Analysed tumour and normal samples without making any adjustments to the applied test","1. Read counts for both alleles. 2. SNV file"]
[null,"Bailey et al., 2015","ABC","ASB","No","MCF7 and GM12878","Binomial test","Uses the observed gDNA as the expected occurrence of the two alleles.","1. Sorted Chip-seq BAM/SAM file. 2 SNV file"]
[null,"Chen et al., 2016","AlleleDB","Both","No","gEUVADIs (RNA-seq) and ENCODE (ChIP-seq)","Beta-binomial model","Filter out heterozygous sites if they lie in regions predicted to be copy number variants as determined by the read depth of the genome sequencing data","Web repository based on AlleleSeq"]
[null,"Liu et al., 2016","cisASE","ASE","No","Paired human colon tumornormal\nsamples (Seshagiri, et al., 2012),  mouse colon carcinoma cell line (Castle, et al., 2014) and NA12878","Likelihood ratio test","Use allele frequecy from additonal DNA sequencing data as the expected occurrence of the two alleles ","1. DNA-seq and RNA-seq pileup files. 2. SNV file. 3. Anotation and Phasing file (optional) files for gene level ASE detection "]
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[null,"This table shows the heterogeneity in eleven studies performing allele-specific mapping analyses using different tools and strategies, "]
[null,"e.g. variations of statistical tests, required coverage threshold for statistical testing, and different strategies to deal with heterozygous sites in regions of altered copy number"]