{"text_format":"2","workbook":"xlsx","n_sheets":1,"sheets":["TableS17B"],"not_rendered":{"charts":0,"images":0,"macros":0,"external_links":0,"defined_names":0,"comments":0,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1904"}

{"sheet":"TableS17B","index":0,"n_rows":78,"n_cols":11,"rows_kept":78,"cut":false,"hidden":false,"merged":[[77,0,77,10]]}
["Sample group","Sample ID","Status","Sex","Family type","DNA source","Cytoband","Anomaly type","Karyotype","Comments ","CNV calls"]
["Parents"]
["Stage 1 (Pinto et al.)","1108_2","Father","M","MPX","CL","2p","2p arm BAF split","N/A","Mosaicism"]
["Stage 1 (Pinto et al.)","5008_1","Mother","F","MPX","CL","5q14.3-telom","5q arm high intensity, BAF split","N/A","Partial duplication (5q14.3-telom); NOT found in another DNA batch by Affy500K-EA"]
["Stage 1 (Pinto et al.)","14217_3491","Mother","F","SPX","Blood","9q-telom","9q arm BAF split","N/A","Mosaicism"]
["Stage 1 (Pinto et al.)","14123_2171","Mother","F","SPX","Blood","11p12-telom","11p arm BAF split","N/A","Mosaicism"]
["Stage 1 (Pinto et al.)","3047_1","Father","M","MPX","Buccal","BAF split 12","High intensity, BAF split","N/A","Whole chr 12 duplication"]
["Stage 1 (Pinto et al.)","1163_2","Father","M","MPX","CL",14,"High intensity, BAF split","N/A","Whole chr 14 duplication"]
["Stage 1 (Pinto et al.)","1763_211","Father","M","MPX","CL","14q12-q32.33","14q arm high intensity, BAF split","N/A","Partial duplication (14q12-q32.33)"]
["Stage 1 (Pinto et al.)","9518_102","Father","M","MPX","Unknown",16,"High intensity, BAF split","N/A","Whole chr 16 duplication"]
["Stage 1 (Pinto et al.)","5355_2","Father","M","SPX","Blood","22q11.21-telom","22q arm BAF split ","N/A","Mosaicism"]
["Stage 1 (Pinto et al.)","1341_1","Mother","F","MPX","CL","X","Female low X intensity, BAF split","XX.X0","Mosaicism"]
["Stage 1 (Pinto et al.)","3100_2","Mother","F","MPX","Buccal","X","Female high X intensity, BAF split","XX.XXX","Mosaicism"]
["Stage 1 (Pinto et al.)","5134_1","Mother","F","MPX","CL","X","BAF split","XX.X0","Mosaicism; NOT found in another DNA batch by Affy500K"]
["Stage 1 (Pinto et al.)","5294_1","Mother","F","SPX","Blood","X","Female low X intensity, BAF split","XX.X0","Mosaicism; NOT found in another DNA batch by Affy500K"]
["Stage 2","18174_202","Mother","F","SPX","CL","7q","Whole 7q arm BAF split (no LRR deflection)","N/A","Mosaicism, not transmitted"]
["Stage 2","6120_1","Mother","F","SPX","CL","11 qterm","Chr 11q-term DUP (qterm)","N/A","Not transmitted"]
["Stage 2","17027_6","Mother","F","MPX","Blood",12,"Whole chr 12 DUP","N/A","Not transmitted"]
["Stage 2","14381_4941","Mother","F","SPX","CL",12,"Whole chr 12 DUP","N/A","Not transmitted"]
["Stage 2","16070_2211026003","Father","M","SPX","Blood",12,"Whole chr 12 DUP (LRR deflection, no BAF split)","N/A","Not transmitted"]
["Stage 2","16058_2211037002","Mother","F","SPX","CL",12,"Whole chr 12 DUP (LRR deflection, no BAF split)","N/A","Not transmitted"]
["Stage 2","18182_202","Mother","F","SPX","CL","X","Whole chr X DUP (LRR defelection, BAF split)","N/A","Not transmitted"]
["Stage 2","20106_1487011","Mother","F","SPX","CL","X","Whole chr X DUP (LRR deflection, BAF split)","N/A","Not transmitted"]
["Stage 2","18173_202","Mother","F","SPX","CL","X","Whole chr X DUP (LRR defelection, BAF split)","N/A","Not transmitted"]
["Stage 2","21012_2","Mother","F","SPX","CL","X","Whole chr X DUP (LRR deflection, BAF split","N/A","Not transmitted"]
["Stage 2","6293_2","Mother","F","SPX","Blood","X","Whole chr X DUP (BAF split)","N/A","Not transmitted"]
["Stage 2","18092_201","Father","M","UNK","CL","7q34-q36.3","16 Mb DUP at 7q35-q36.3 (no visible LRR deflection)","N/A","Not transmitted; mosaic","chr7:142193132-158735112 (merged) "]
["Stage 2","16071_2211032002","Mother","F","SPX","Blood","8p12-q11.1","11Mb p-q DUP at 8p12-8q11.1 (gain|plus_loss_within_gain)","N/A","Ring chr?, not transmitted ","chr8:36164852-47354331 (merged)"]
["Stage 2","4197_1001","Mother","F","MPX","CL","X","Whole chr BAF split (no visible LRR deflection)","N/A","Mosaicism"]
["Controls"]
["SAGE controls (Pinto et al.)","B453672_1007871661","Control","F","–","CL","7p22.3-7p21.2","High intensity, BAF split","N/A","Partial duplication (14.56 Mb; telom-7p21.2)"]
["SAGE controls (Pinto et al.)","B192507_1007872574","Control","M","–","CL","10q21.1-q22.1","High intensity, BAF split","N/A","Partial duplication (17.9 Mb; 10q21.1-q22.1)"]
["SAGE controls (Pinto et al.)","B538284_1007874460","Control","F","–","CL","12q24.31-q24.33","Low intensity, BAF split","N/A","Partial deletion (11 Mb; 12q24.31-q24.33)"]
["SAGE controls (Pinto et al.)","B875847_1007874425","Control","F","–","CL","12q14-telom","BAF split","N/A","Mosaicism"]
["SAGE controls (Pinto et al.)","B712092_1007853733","Control","M","–","CL","19q13.2-telom","BAF split","N/A","Mosaicism"]
["SAGE controls (Pinto et al.)","B272418_1007873376","Control","F","–","CL","X","Female low X intensity","X0","Turner syndrome karyotype"]
["SAGE controls (Pinto et al.)","B331706_1007843500","Control","F","–","CL","X","Female low X intensity","X0","Turner syndrome karyotype"]
["SAGE controls (Pinto et al.)","B182886_0057061564","Control","F","–","CL","X","BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B227532_1007875264","Control","F","–","CL","X","Female low X intensity, BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B363038_1007872238","Control","F","–","CL","X","Female low X intensity, BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B400207_1007874431","Control","F","–","CL","X","BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B442361_1007872258","Control","F","–","CL","X","BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B443117_1007872671","Control","F","–","CL","X","Female low X intensity, BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B449686_1007840765","Control","F","–","CL","X","BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B617470_1007872267","Control","F","–","CL","X","BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B650091_1007872185","Control","F","–","CL","X","BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B709845_1007875224","Control","F","–","CL","X","BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B717554_1007875274","Control","F","–","CL","X","Female low X intensity, BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B729328_1007872228","Control","F","–","CL","X","BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B821840_1007852894","Control","F","–","CL","X","Female low X intensity, BAF split","XX.X0","Turner syndrome karyotype, mosaicism"]
["SAGE controls (Pinto et al.)","B747337_1007873392","Control","M","–","CL","XY","Male median low Y intensity","XY.X0","45,X/46,XY mosaicism"]
["SAGE controls (Pinto et al.)","B888881_1007873634","Control","M","–","Blood","XY","Multiple anomalies in chrX and chrY","XY/XXY/XYY","Mosaicism"]
["SAGE controls (Pinto et al.)","B915478_1007845341","Control","M","–","Blood","X","Male high X intensity","XXY","–"]
["OC controls","110036010965_","Control","M","–","Blood","13,9","Duplication/deletion","N/A","chr 13 - multiple segments of gains or losses; chr 9 - BAF split"]
["OC controls","110036015436_","Control","M","–","Blood","1p, 13","13q partial arm BAF split, no visible LRR deflection; 1p partial arm BAF split, no visible LRR deflection","N/A","13q partial arm mosaicism; 1p partial arm mosaicism"]
["OC controls","110036024610_","Control","F","–","Blood","3p","Partial arm 3p BAF split, no visible LRR deflection","N/A","3p partial arm mosaicism"]
["OC controls","110036024990_","Control","M","–","Blood",12,"Whole chr 12 DUP","N/A","Trisomy chomosome 12"]
["HABC controls","HABC_901504_901504","Control","M","–","Blood",13,"Complex BAF and LRR pattern shifts","N/A","Mosaicism; mosaic deletions with gradual increase in the % of mosaicism"]
["HABC controls","HABC_902472_902472","Control","M","–","Blood","XY","BAF split within PAR regions & rest of chrX; clear intensity deflection; whole chrX duplication","XXYY","Mosaicism"]
["HABC controls","HABC_900984_900984","Control","M","–","Blood","Y","BAF split limited to PAR regions","XYY"]
["HABC controls","HABC_901023_901023","Control","M","–","Blood","Y","BAF split limited to PAR regions","XYY"]
["HABC controls","HABC_900891_900891","Control","F","–","Blood","1, 6p, 8p, 8q, 12, 18p, 18q, 20, X","multiple anomalies in various chromosomes: chr1 BAF split & intensity shift, 6p BAF split, 8p and 8q(partial) BAF split & intensity shift, chr12 BAF split, 18p and 18q (partial) BAF split & intensity shift, chr20: BAF split; Xp: BAF split & intensity shift","N/A","chr1 duplication, 6p mosaicism, 8p and 8q partial duplication, chr12 mosaicism, 18p and 18q partial duplication, chr20 mosaicism, Xp duplication"]
["HABC controls","HABC_900640_900640","Control","M","–","Blood","4q, 9p","4q BAF split, 9p BAF split","N/A","Mosaicism"]
["HABC controls","HABC_901972_901972","Control","M","–","Blood","9p","BAF split","N/A","9p mosaicism"]
["HABC controls","HABC_900371_900371","Control","M","–","Blood",9,"BAF split","N/A","Mosaicism"]
["HABC controls","HABC_900882_900882","Control","M","–","Blood",12,"chr12 BAF split; 8q BAF split & high intensity","N/A","8q duplication, chr12 mosaicism"]
["HABC controls","HABC_900960_900960","Control","M","–","Blood",12,"BAF split & high intensity","N/A","Whole chr 12 duplication"]
["HABC controls","HABC_900027_900027","Control","F","–","Blood",12,"BAF split & slight high intensity","N/A","Whole chr 12 duplication"]
["HABC controls","HABC_901076_901076","Control","M","–","Blood",12,"BAF split & high intensity","N/A","Whole chr 12 duplication"]
["HABC controls","HABC_901227_901227","Control","M","–","Blood",12,"BAF split & high intensity","N/A","Whole chr 12 duplication"]
["HABC controls","HABC_901689_901689","Control","F","–","Blood","12p","BAF split","N/A","12p mosaicism"]
["HABC controls","HABC_900502_900502","Control","M","–","Blood","13, 17p","chr13 complex BAF and intensity pattern, 17p BAF split & low intensity","N/A","multiple anomalies in chr 13, 17 p deletion"]
["HABC controls","HABC_901049_901049","Control","M","–","Blood","X","BAF split","N/A","Mosaicism"]
["HABC controls","HABC_901997_901997","Control","F","–","Blood",15,"15p and 15q partial complex BAF spit","N/A","15p and 15q partial mosaicism"]
["HABC controls","HABC_901198_901198","Control","M","–","Blood","16q","BAF split","N/A","16q partial mosaicism"]
["HABC controls","HABC_900747_900747","Control","M","–","Blood","multiple","multiple anomalies in various chromosomes","N/A","Mosaicism"]
["HABC controls","HABC_901269_901269","Control","M","–","Blood","X","BAF split","N/A","Mosaicism"]
["Samples including ASD families and controls that passed QC filters but showed CNVs by any algorithm larger than 7.5 Mb, long runs of homozygosity, or CNVs encompassing/or close to the centromere, on any of the autosomes or chrX were further inspected manually by plotting their log2 ratio intensities as well as allelic genotype ratios. A  cutoff of >7.5 Mb was selected to be consistent with large cytogenetically visible chromosome abnormalities. Samples containing such alterations were excluded from the analyses.\nAbbreviations: BAF, B allele frequency; EA: early access (Affy500K-EA vs. Affy500K); CL, cell line; MPX, multiplex; N/A, not available; SPX, simplex; UNK, unknown family type (extended family not evaluated for ASD)\nChromosome abnormalities in probands are listed in Table S1C."]