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{"sheet":"Table S17C","index":0,"n_rows":457,"n_cols":16,"rows_kept":457,"cut":false,"hidden":false,"merged":[]}
["Stage","AGP ID","Sex","Family type","DNA source array ","DNA source validation ","Estimated_ancestry","Cytoband","Chr:start-end (hg18)","Size (bp)","CNV","RefSeq genes","Inheritance","Validation method","Segregation in sibs","Comment"]
["Stage 1","2232_1","Male","SPX","Blood","Blood","European","1p36.33","1:1370430-1429557",59128,"Loss","ATAD3B, ATAD3C","Paternal","qPCR","(not tested)"]
["Stage 1","6356_5","Male","SPX","UNK (blood or CL)","Blood","European","1p36.32-p36.33","1:2118508-2325536",207029,"Loss","C1orf86, LOC100129534, MORN1, RER1, SKI","De novo","qPCR","(2 healthy sibs, no DNA)"]
["Stage 2","17002_1","Male","SPX","CL","CL","Other","1p36.21","1:12730924-12783336",52413,"Loss","C1orf158, PRAMEF1, PRAMEF12","Maternal","qPCR","(not tested)"]
["Stage 1","6317_5","Male","SPX","Blood","Blood","European","1p36.11","1:26767083-26941756",174674,"Gain","ARID1A, RPS6KA1","Paternal","qPCR","(2 sibs, no DNA)"]
["Stage 1","14239_2920","Male","SPX","Blood","Blood","European","1p33","1:49685647-49770826",85180,"Loss","AGBL4 intronic","Maternal","qPCR","(no siblings)"]
["Stage 1","14080_1360","Female","SPX","Blood","Blood","European","1p33","1:49688435-49770826",82392,"Loss","AGBL4 intronic","Paternal","qPCR","(1 healthy sister, 1 healthy brother, no DNA)"]
["Stage 1","14244_3680","Male","SPX","Blood","Blood","European","1p33","1:49688435-49770826",82392,"Loss","AGBL4 intronic","Maternal","qPCR","(no siblings)"]
["Stage 1","14246_3700","Male","SPX","Blood","Blood","European","1p33","1:49688435-49770826",82392,"Loss","AGBL4 intronic","Maternal","qPCR","(no siblings)"]
["Stage 2","14381_4940","Male","SPX","CL","CL","European","1p31.3","1:61053139-61093982",40844,"Gain","—","Maternal","qPCR","(not tested)"]
["Stage 1","6180_4","Male","SPX","Blood","Blood","European","1p31.1","1:75508955-75788048",279094,"Loss","SLC44A5","Maternal","qPCR","(1 unaffected sister, no DNA)"]
["Stage 2","8658_201","Female","SPX","Blood","Blood","European","1p21.2-p21.3","1:98175622-100923952",2748331,"Loss","18 genes, including AGL, LPPR4, LPPR5, MIR137, MIR553 and SNX7","De novo","qPCR","(2 healthy siblings, not tested)"]
["Stage 2","9877_204","Male","SPX","Blood","Blood","Other","1p21.2-p21.3","1:98247355-99645560",1398206,"Gain","LOC100129620, LPPR4, LPPR5, MIR137, SNX7","De novo","qPCR","(3 siblings, not tested)"]
["Stage 2","14310_4270","Male","SPX","Blood","Blood","European","1p21.1","1:105623065-105788728",165664,"Gain","—","De novo","qPCR","(not tested)"]
["Stage 2","14310_4270","Male","SPX","Blood","Blood","European","1p21.1","1:105896243-106480692",584450,"Gain","—","De novo","qPCR","(not tested)"]
["Stage 2","20111_1517001","Male","MPX","Blood","Blood","Other","1p13.2","1:111793666-111826604",32939,"Gain","ATP5F1, C1orf162","Paternal","qPCR","no CNV in affected sib"]
["Stage 2","16035_1571013001","Male","MPX","CL","CL","European","1q21.1","1:144482933-146325557",1842625,"Gain","1q21.1 duplication syndrome (including CHD1L and GJA5)","De novo","qPCR","(brother with Asperger syndrome, not tested)"]
["Stage 1","1952_301","Male","MPX","CL","CL","Other","1q21.1","1:144500467-146336720",1836254,"Gain","1q21.1 duplication syndrome (including CHD1L and GJA5)","De novo","qPCR","absent in affected sister"]
["Stage 2","8635_201","Male","MPX","Blood","Blood","European","1q21.1","1:144500467-146377870",1877404,"Loss","1q21.1 deletion syndrome (including CHD1L and GJA5)","De novo","qPCR","(1 sister with epilepsy and unilateral deafness and 1 healthy sister, not tested)"]
["Stage 1","13135_1523","Female","UNK","Blood","Blood","European","1q21.1","1:144838594-146308287",1469694,"Gain","1q21.1 duplication syndrome (including CHD1L and GJA5)","De novo","qPCR","(1 brother with Asperger and dyspraxia, not tested)"]
["Stage 2","4291_1","Male","MPX","Blood","Blood","European","1q21.1","1:144967972-146317915",1349944,"Gain","1q21.1 duplication syndrome (including CHD1L and GJA5)","Maternal","qPCR (Griswold et al. 2011, PMID: 21360829)","not present in affected sib"]
["Stage 2","6336_4","Male","SPX","Blood","Blood","European","1q22","1:153855744-153992914",137171,"Loss","DAP3, GON4L, MSTO2P, YY1AP1","Maternal","qPCR","(1 healthy sister, no DNA)"]
["Stage 1","3051_4","Male","MPX","Buccal","Buccal","European","1q23.2","1:158188993-158199760",10768,"Loss","SLAMF9","Maternal","LR-PCR and sequencing","CNV also present in unaffected sister, absent in affected brother"]
["Stage 1","13041_503","Male","UNK","Blood","Blood","European","1q24.2","1:167493526-167507362",13837,"Loss","NME7 intronic","De novo","qPCR","(not tested)"]
["Stage 1","2230_1","Male","SPX","Blood","Blood","European","1q24.2","1:167493526-167507362",13837,"Loss","NME7 intronic","Maternal","qPCR","(not tested)"]
["Stage 1","6340_3","Male","SPX","Blood","UNK (blood or CL)","European","1q25.1","1:172142024-172310899",168876,"Gain","RC3H1, SERPINC1","Paternal","qPCR","(3 sibs, no DNA)"]
["Stage 2","9770_201","Male","SPX","Blood","Blood","Other","1q42.12","1:222974403-223075204",100802,"Gain","CNIH3","Maternal","qPCR","(not tested)"]
["Stage 1","13133_1503","Male","UNK","Blood","Blood","European","1q42.2","1:229977634-230015444",37811,"Gain","DISC1, TSNAX-DISC1","Maternal","qPCR","(1 healthy sister, no DNA)"]
["Stage 1","5467_3","Male","SPX","Blood","Blood","Other","1q42.3-1q44","1:233476547-247165725",13689179,"Gain","13 Mb 1q42-q44 duplication (114 genes), chromosomal abnormality","De novo","qPCR","(1 non-ASD brother, not tested)","chromosomal abnormality, excluded from main analyses"]
["Stage 2","9770_201","Male","SPX","Blood","Blood","Other","1q44","1:246489811-246602656",112846,"Gain","OR14C36, OR2M7, OR2T12, OR2T33, OR2T4","Maternal","qPCR","(not tested)"]
["Stage 1","13082_963","Male","UNK","Blood","Blood","European","2p25.1","2:11712589-11741036",28448,"Gain","NTSR2","De novo","qPCR","(not tested)"]
["Stage 1","3215_3","Male","MPX","CL","CL","Other","2p22.2","2:37412859-37449029",36171,"Loss","QPCT","Maternal","LR-PCR and sequencing","also present in affected brother"]
["Stage 2","16074_1571042001","Male","SPX","CL","CL","European","2p16.3","2:50037898-50407550",369653,"Loss","NRXN1","Maternal","qPCR","(sib ADHD not tested)"]
["Stage 1","14068_1180","Male","SPX","Blood","Blood","European","2p16.3","2:50493827-50677835",184009,"Gain","NRXN1","De novo","qPCR","(1 healthy sister, not tested)"]
["Stage 1","13017_223","Female","UNK","Blood","Blood","European","2p16.3","2:50539877-50730546",190670,"Loss","NRXN1","De novo","qPCR","(not tested)"]
["Stage 1","5236_3","Female","MPX","Blood","Blood","Other","2p16.3","2:50705521-50719594",14074,"Loss","NRXN1","Maternal","Agilent 1M, qPCR","1 ASD brother, no CNV"]
["Stage 1","6125_4","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","2p16.3","2:50822312-50886363",64052,"Loss","NRXN1 intronic","Maternal","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","6197_4","Female","MPX","Blood","Blood","European","2p16.3","2:50822312-50900862",78551,"Gain","NRXN1 intronic","Maternal","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","5072_3","Male","MPX","CL","CL","European","2p16.3","2:50912249-50955087",42839,"Loss","NRXN1 intronic","Maternal","qPCR, Illumina 1M-duo for sib","present in 1 brother with autism"]
["Stage 2","13216_2383","Male","UNK","Blood","Blood","European","2p16.3","2:50968208-51214171",245964,"Loss","NRXN1","De novo","qPCR","(not tested)"]
["Stage 1","13153_1703","Male","UNK","Blood","Blood","European","2p16.3","2:50990306-51222043",231738,"Loss","NRXN1","De novo","qPCR","(3 sibs, not tested)"]
["Stage 1","13037_463","Male","SPX","Blood","Blood","European","2p16.3","2:51002576-51157742",155167,"Loss","NRXN1","De novo","qPCR","(not tested)"]
["Stage 1","5328_3","Male","SPX","CL","CL","Other","2p16.3","2:51044181-51120644",76464,"Loss","NRXN1","Paternal","Agilent 1M, qPCR","1 non-ASD sister, CNV; 1 non-ASD brother, no CNV"]
["Stage 2","17027_1","Male","MPX","Blood","Blood","European","2p16.3","2:51076611-51147600",70990,"Loss","NRXN1","Paternal","qPCR","CNV also present in affected brother"]
["Stage 2","9801_202","Male","SPX","Blood","Blood","Other","2p16.1","2:56377838-56407882",30045,"Loss","CCDC85A intronic","Paternal","qPCR","(not tested)"]
["Stage 1","3017_3","Male","MPX","CL","Blood","European","2p12","2:76782603-76809810",27208,"Loss","— (downstream of LRRTM4)","Paternal","LR-PCR","absent in 1 affected brother"]
["Stage 1","3092_3","Female","MPX","CL","Blood","European","2p12","2:76782603-76809810",27208,"Loss","— (downstream of LRRTM4)","Maternal","LR-PCR","absent in 1 affected brother"]
["Stage 1","3106_3","Male","MPX","CL","Blood","European","2p12","2:76782603-76809810",27208,"Loss","— (downstream of LRRTM4)","Paternal","LR-PCR","absent in 1 unaffected brother and 1 affected sister"]
["Stage 1","3160_3","Male","MPX","Buccal","Blood","European","2p12","2:76782603-76809810",27208,"Loss","— (downstream of LRRTM4)","Paternal","LR-PCR","present in 1 affected sister"]
["Stage 2","20000_1010002","Female","SPX","CL","CL","European","2q11.2","2:99204635-99289399",84765,"Gain","LYG1, LYG2","Maternal","qPCR","(not tested)"]
["Stage 1","5089_5","Male","MPX","CL","CL","Other","2q12.1","2:102292943-102345460",52518,"Loss","IL1RL1","De novo","qPCR","MZ twin with autism also carries CNV (1 sister with ASD, no DNA)"]
["Stage 2","3173_3","Male","MPX","Blood","Blood","European","2q13","2:108633306-109881539",1248234,"Gain","10 genes, including ANKRD57, EDAR, LIMS1, RANBP2, SEPT10 and SH3RF3","Paternal","qPCR","CNV in affected sib, no CNV in 2 unaffected sibs"]
["Stage 2","4260_1","Male","SPX","Blood","Blood","European","2q14.2","2:119603876-119882278",278403,"Gain","C1QL2, C2orf76, DBI, STEAP3","De novo","qPCR (Griswold et al. 2011, PMID: 21360829)","(no siblings)"]
["Stage 2","18091_301","Male","MPX","CL","CL","Other","2q21.1","2:130715737-130887269",171533,"Gain","CCDC115, IMP4, PTPN18","Maternal","qPCR","CNV also present in affected sib"]
["Stage 2","8631_201","Male","UNK","Blood","Blood","European","2q21.2","2:132771598-133070297",298700,"Gain","GPR39","Maternal","qPCR","(not tested)"]
["Stage 1","13027_353","Female","UNK","Blood","Blood","European","2q22.3","2:144837809-145315383",477575,"Gain","DKFZp686O1327, ZEB2","De novo","qPCR","(not tested)"]
["Stage 1","3424_3","Male","SPX","Blood","Blood","European","2q23.1","2:148881443-149078468",197026,"Gain","MBD5","Maternal","qPCR","absent in 1 unaffected brother"]
["Stage 2","8496_202","Male","MPX","Blood","Blood","European","2q24.3","2:166994290-167104384",110095,"Loss","SCN7A","Paternal","qPCR","(not tested)"]
["Stage 1","3423_003","Male","SPX","Blood","Blood","European","2q31.1","2:170311824-170375059",63236,"Loss","KLHL23, PHOSPHO2-KLHL23, SSB","Maternal","qPCR","(no siblings)"]
["Stage 2","18182_303","Male","SPX","CL","CL","European","2q32.1","2:184726171-184772645",46475,"Loss","—","Maternal","qPCR","CNV also present in affected sib"]
["Stage 1","14200_3240","Male","SPX","Blood","Blood","European","2q34","2:214803990-214829997",26008,"Gain","SPAG16  intronic","Paternal","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","14164_2680","Male","SPX","Blood","Blood","European","2q34","2:214808080-214829997",21918,"Gain","SPAG16  intronic","Maternal","qPCR","(1 brother language delay, no DNA)"]
["Stage 1","14029_560","Male","SPX","Blood","Blood","European","2q34","2:214808080-214829997",21918,"Gain","SPAG16  intronic","Paternal","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","14301_4220","Male","SPX","Blood","Blood","European","2q34","2:214808080-214829997",21918,"Gain","SPAG16  intronic","Paternal","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","14309_4260","Male","SPX","Blood","Blood","European","2q34","2:214808080-214829997",21918,"Gain","SPAG16  intronic","Paternal","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","5110_3","Male","MPX","Blood","Blood","Other","2q35","2:217291508-217317701",26194,"Gain","—","Paternal","qPCR","(1 brother with autism, not tested)"]
["Stage 2","18173_301","Male","SPX","CL","CL","Other","2q35","2:219391887-219529903",138017,"Gain","PRKAG3, WNT10A, WNT6","Maternal","qPCR","(not tested)"]
["Stage 2","4274_1","Male","SPX","Blood","Blood","European","2q36.3","2:230078358-230181261",102904,"Gain","DNER","Paternal","qPCR (Griswold et al. 2011, PMID: 21360829)","(not tested)"]
["Stage 2","14414_5230","Male","SPX","CL","CL","European","2q36.3","2:230486629-230547253",60625,"Loss","FBXO36, TRIP12","De novo","qPCR","(not tested)"]
["Stage 2","3468_3","Male","SPX","Blood","Blood","European","2q37.1","2:232909572-233017310",107739,"Gain","ALPP, ALPPL2, DIS3L2, ECEL1P2","Maternal","qPCR","(no siblings)"]
["Stage 2","16037_1571015001","Male","SPX","CL","CL","European","2q37.3","2:239765200-239777909",12710,"Loss","HDAC4","Maternal","qPCR, LR-PCR (sequencing coordinates: chr2:239766528-239778481, size 11,954 bp)","(healthy maternal half-brother, not tested)"]
["Stage 2","8415_201","Male","UNK","Blood","Blood","European","2q37.3","2:241999303-242037136",37834,"Gain","FARP2","Paternal","qPCR","(not tested)"]
["Stage 2","4374_1","Male","SPX","Blood","Blood","European","3p26.3","3:36044-1633491",1597448,"Loss","CHL1, CNTN6","Paternal","qPCR (Griswold et al. 2011, PMID: 21360829)","(not tested)"]
["Stage 2","16095_1571145001","Male","SPX","CL","CL","European","3p26.3","3:1697281-1733089",35809,"Loss","—","Maternal","qPCR","(not tested)"]
["Stage 1","5355_3","Male","SPX","Blood","Blood","European","3p26.3","3:1978504-2151165",172662,"Gain","CNTN4","Maternal","qPCR, Illumina 1M-duo for sib","present in 1 non-ASD sister"]
["Stage 1","5269_3","Male","SPX","Blood","Blood","European","3p26.3","3:2644708-2876647",231940,"Gain","CNTN4","Paternal","qPCR, Illumina 1M-duo for sib","present in 1 non-ASD brother"]
["Stage 1","5267_3","Male","SPX","Blood","Blood","European","3p26.3","3:3098326-3184518",86193,"Loss","CRBN, IL5RA, TRNT1","Paternal","qPCR","(1 non-ASD sister, no DNA)"]
["Stage 1","3319_3","Female","MPX","Buccal","Buccal","European","3p26.2","3:4063576-4076356",12781,"Loss","—","Maternal","LR-PCR","present in 1 of 2 unaffected sisters but not in affected sister "]
["Stage 1","3211_3","Male","MPX","Buccal","Blood","European","3p26.2","3:4069293-4236304",167012,"Loss","—","Paternal","LR-PCR","absent in 1 affected brother"]
["Stage 2","3616_3","Male","UNK","Blood","Blood","European","3p25.3","3:9474320-9498362",24043,"Loss","SETD5","De novo","qPCR","(1 non-ASD brother, not tested)"]
["Stage 1","5220_3","Female","SPX","Blood","Blood","European","3p24.3","3:19127998-19640299",512302,"Gain","KCNH8","De novo","qPCR, Agilent 1M","(1 non-ASD maternal half-sister, no DNA)"]
["Stage 1","3174_3","Male","MPX","Buccal","Blood","European","3p24.3","3:19921061-20096832",175772,"Loss","C3orf48, EFHB, KAT2B, RAB5A","De novo","qPCR","absent in 1 brother with autism"]
["Stage 2","18168_302","Male","SPX","CL","CL","European","3p14.2","3:60043770-60251762",207993,"Loss","FHIT intronic","Maternal","qPCR","(not tested)"]
["Stage 2","20000_1010002","Female","SPX","CL","CL","European","3p12.1","3:85622506-85711555",89050,"Loss","CADM2 intronic","Maternal","qPCR","(not tested)"]
["Stage 1","2232_1","Male","SPX","Blood","Blood","European","3p11.1","3:89485137-89499861",14725,"Loss","EPHA3 intronic","both parents","qPCR, Affy 6.0","(not tested)"]
["Stage 1","6203_4","Male","SPX","Blood","Blood","Other","3q11.2","3:94994003-95230688",236686,"Gain","ARL13B, PROS1, STX19","Maternal","qPCR","absent in 1 unaffected brother"]
["Stage 1","14210_3370","Male","SPX","Blood","Blood","European","3q11.2","3:98454493-98508607",54115,"Loss","EPHA6 intronic","Paternal","qPCR","(not tested)"]
["Stage 1","14265_3880","Male","SPX","Blood","Blood","European","3q11.2","3:98454493-98508607",54115,"Loss","EPHA6 intronic","Paternal","qPCR","(not tested)"]
["Stage 2","20032_1226001","Male","MPX","Blood","Blood","European","3q12.2-q13.11","3:101854561-106110833",4256273,"Loss","17 genes, including GPR128, NFKBIZ, PCNP, RG9MTD1, RPL24 and SENP7","Maternal","qPCR","deletion present in affected brother (20032_1226021) and affected sister (20032_122602), both with broad autism spectrum"]
["Stage 1","5245_3","Male","MPX","CL","CL","European","3q13.31","3:117285007-117477191",192185,"Loss","LSAMP","De novo","qPCR, Agilent 1M (seems mosaic)","1 sister with ASD, no CNV detected by qPCR"]
["Stage 1","3084_3","Male","MPX","Buccal","Buccal","European","3q13.33","3:120845429-120850038",4610,"Loss","POPDC2","Maternal","LR-PCR and sequencing","no CNV in affected brother"]
["Stage 2","8587_210","Female","UNK","Blood","Blood","European","3q22.3","3:139760896-140127703",366808,"Gain","CEP70, FAIM, PIK3CB","De novo","qPCR","(not tested)"]
["Stage 1","3011_3","Male","MPX","CL","CL","European","3q25.2","3:155234829-155370454",135626,"Loss","ARHGEF26, LOC100507524","Paternal","LR-PCR and sequencing","no CNV in affected sib"]
["Stage 1","13046_553","Male","UNK","Blood","Blood","European","3q26.1","3:164004033-164101579",97547,"Loss","—","De novo","qPCR","(not tested)"]
["Stage 1","13108_1253","Male","UNK","Blood","Blood","European","3q26.1","3:164004033-164101579",97547,"Loss","—","De novo","qPCR","(not tested)"]
["Stage 1","5210_4","Male","MPX","Blood","Blood","European","3q26.31","3:174722147-174771975",49829,"Gain","NLGN1 intronic","Paternal","qPCR","(1 brother with ASD, not tested; 1 baby sister, no phenotype data, no DNA)"]
["Stage 2","18116_302","Male","MPX","CL","CL","European","3q27.2","3:186264896-186313382",48487,"Gain","C3orf70","Unknown (not maternal, father no DNA)","qPCR","no CNV in affected sib"]
["Stage 2","8588_201","Male","UNK","Blood","Blood","European","3q29","3:195971510-197675831",1704322,"Loss","20 genes, including ACAP2, PCYT1A, PPP1R2, SDHAP1, SDHAP2 and ZDHHC19","De novo","qPCR","(no siblings)"]
["Stage 2","21020_1","Male","SPX","CL","Blood","European","4p16.1-p16.3","4:53403-9016339",8962937,"Gain","8.9 Mb 4p16.3-p16.1 duplication (116 genes), chromosomal abnormality (unbalanced translocation)","De novo","qPCR, FISH","(not tested)","chromosomal abnormality, excluded from main analyses"]
["Stage 1","3388_4","Female","MPX","Buccal","Buccal","Other","4p15.32","4:15333541-15411016",77476,"Loss","BST1, CD38","Maternal","LR-PCR and sequencing","absent in affected sister"]
["Stage 1","5070_4","Male","MPX","Blood","Blood","European","4p15.31","4:20944461-20960842",16382,"Loss","KCNIP4 intronic","Paternal","qPCR","(1 brother with ASD, not tested)"]
["Stage 2","2190_1","Male","SPX","Blood","Blood","European","4p12","4:47358807-47447311",88505,"Gain","CORIN","Paternal","qPCR","(not tested)"]
["Stage 1","13022_293","Male","UNK","Blood","Blood","European","4q13.1","4:63820936-63833261",12326,"Loss","—","De novo","qPCR","(not tested)"]
["Stage 2","16095_1571145001","Male","SPX","CL","CL","European","4q22.1","4:90711789-90746801",35013,"Gain","—","Maternal","qPCR","(not tested)"]
["Stage 2","8677_201","Male","SPX","Blood","Blood","Other","4q22.2","4:94659049-95289667",630619,"Gain","ATOH1, GRID2","De novo","qPCR","(not tested)"]
["Stage 2","14381_4940","Male","SPX","CL","CL","European","4q22.3","4:96580176-96620670",40495,"Loss","UNC5C  intronic","Maternal","qPCR","(not tested)"]
["Stage 2","6402_3","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","4q22.3-q23","4:98781694-99627129",845436,"Gain","C4orf37, RAP1GDS1, TSPAN5","De novo","qPCR","(3 siblings, no DNA)"]
["Stage 1","3192_3","Male","MPX","Buccal","Buccal","European","4q24","4:106685577-106718221",32645,"Loss","ARHGEF38","Paternal","LR-PCR","CNV also present in affected brother"]
["Stage 2","6413_4","Male","SPX","Blood","Blood","European","4q26-q27","4:120446867-121182849",735983,"Gain","FABP2, FLJ14186, LOC645513, PDE5A","Maternal","qPCR","absent in unaffected sib"]
["Stage 1","6356_5","Male","SPX","UNK (blood or CL)","Blood","European","4q31.1","4:140478322-140522239",43918,"Loss","NAA15","Paternal","qPCR","(2 healthy sibs, no DNA)"]
["Stage 1","3032_3","Male","MPX","CL","CL","European","4q31.23","4:149049922-149104066",54145,"Loss","ARHGAP10","Paternal","LR-PCR and sequencing","CNV also present in affected brother"]
["Stage 1","3072_008","Male","MPX","CL","Blood","European","4q35.2","4:189540090-190704726",1164637,"Loss","HSP90AA4P, LOC401164","Paternal","qPCR","(1 affected cousin in maternal side of family, not tested)"]
["Stage 1","3072_008","Male","MPX","CL","Blood","European","4q35.2","4:190922297-190993476",71180,"Loss","—","Paternal","qPCR","(1 affected cousin in maternal side of family, not tested)"]
["Stage 1","6033_3","Male","MPX","Blood","Blood","European","5p14.3","5:19532212-20357961",825750,"Loss","CDH18","Maternal","qPCR","absent in 1 sister with autism"]
["Stage 1","2241_1","Male","SPX","Blood","Blood","European","5p14.2","5:24545450-24623946",78497,"Loss","CDH10","Maternal","qPCR","(not tested)","array failed QC, CNV validated"]
["Stage 1","5332_3","Male","SPX","CL","CL","European","5p12","5:43037358-43096689",59332,"Loss","C5orf39, LOC153684, LOC648987","Maternal","qPCR, Illumina 1M-duo for sibs","1 non-ASD twin brother (5332_5, zygosity unknown) and 1 non-ASD brother (5332_4), no CNV in either"]
["Stage 1","2230_1","Male","SPX","Blood","Blood","European","5q11.2","5:54842833-54966863",124031,"Gain","PPAP2A, RNF138P1, SLC38A9","Paternal","qPCR, Affy 6.0","(not tested)"]
["Stage 2","18116_302","Male","MPX","CL","CL","European","5q14.3","5:85426407-85482668",56262,"Gain","—","Unknown (not maternal, father no DNA)","qPCR","no CNV in affected sib"]
["Stage 2","8709_201","Female","SPX","Blood","Blood","European","5q14.3","5:88588170-89505509",917340,"Loss","MIR3660","De novo","qPCR","no CNV in unaffected sister"]
["Stage 2","8540_201","Male","UNK","Blood","Blood","European","5q15","5:93093905-93140711",46807,"Loss","FAM172A, POU5F2","Paternal","qPCR","CNV in male sib (22733)"]
["Stage 2","9770_201","Male","SPX","Blood","Blood","Other","5q21.1","5:99352709-99474012",121304,"Loss","—","Maternal","qPCR","(not tested)"]
["Stage 2","20164_1684001","Male","SPX","Blood","Blood","European","5q21.1","5:101039214-101123914",84701,"Gain","—","Maternal","qPCR","(no siblings)"]
["Stage 1","14054_930","Male","SPX","Blood","Blood","European","5q22.1","5:110263975-110789999",526025,"Gain","CAMK4, TSLP, WDR36","Paternal","qPCR","(not tested)"]
["Stage 1","14061_1040","Male","SPX","Blood","Blood","European","5q23.1","5:118544777-118617384",72608,"Gain","DMXL1","Maternal","qPCR","(no siblings)"]
["Stage 2","8418_201","Male","UNK","Blood","Blood","European","5q33.1","5:147963048-148010257",47210,"Gain","HTR4","Maternal","qPCR","(not tested)"]
["Stage 2","3616_3","Male","UNK","Blood","Blood","European","5q35.3","5:176510678-176531722",21045,"Loss","NSD1 intronic","Paternal","qPCR","(not tested)"]
["Stage 1","13007_83","Male","UNK","Blood","Blood","European","6p25.3","6:757136-794087",36952,"Gain","—","De novo","qPCR","(not tested)"]
["Stage 2","18097_301","Male","MPX","CL","CL","European","6p22.3","6:20811931-20937751",125821,"Loss","CDKAL1","Paternal","qPCR","CNV also present in affected sib"]
["Stage 2","20042_1249001","Male","SPX","Blood","Blood","European","6p22.2","6:23847641-23883847",36207,"Loss","—","Paternal","qPCR","(no siblings)"]
["Stage 2","20042_1249001","Male","SPX","Blood","Blood","European","6p22.2","6:23847641-23883847",36207,"Loss","—","Maternal","qPCR","(not tested)"]
["Stage 1","5521_3","Male","SPX","Blood","Blood","European","6p22.1","6:26240643-26359580",118938,"Gain","histone gene cluster (15 genes)","Maternal","qPCR","2 non-ASD sisters, no CNV in either"]
["Stage 2","18091_301","Male","MPX","CL","CL","Other","6p22.1","6:29192211-29259291",67081,"Gain","OR2J2","Maternal","qPCR","CNV also present in affected sib"]
["Stage 1","5353_3","Female","SPX","Blood","Blood","European","6p21.32","6:33399849-33512042",112194,"Loss","CUTA, KIFC1, PHF1, SYNGAP1","De novo","qPCR","(2 non-ASD brothers and 1 non-ASD sister, not tested)"]
["Stage 2","20054_1280001","Male","SPX","Blood","Blood","European","6p21.2","6:38229189-38315614",86426,"Gain","BTBD9, ZFAND3","Maternal","qPCR","(not tested)"]
["Stage 2","18133_302","Male","SPX","CL","CL","European","6q12-q13","6:69540429-73375020",3834592,"Gain","13 genes, including B3GAT2, BAI3, LMBRD1, OGFRL1, RIMS1 and SMAP1","De novo","qPCR","(not tested)"]
["Stage 2","18178_302","Male","SPX","CL","CL","European","6q14.1","6:81770234-81939806",169573,"Gain","—","Maternal","qPCR","(not tested)"]
["Stage 2","6248_3","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","6q14.3","6:86352577-86376159",23583,"Loss","SNX14, SYNCRIP","De novo","qPCR","(2 sibs, no DNA)"]
["Stage 1","13094_1113","Male","MPX","Blood","Blood","European","6q21","6:108415352-108444960",29609,"Gain","—","De novo","qPCR","(not tested)"]
["Stage 1","14072_1250","Male","SPX","Blood","Blood","European","6q24.3","6:145841703-145852542",10840,"Loss","—","Paternal","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","14230_3640","Male","SPX","Blood","Blood","European","6q24.3","6:145841703-145857642",15940,"Loss","—","Maternal","qPCR","(2 healthy half-sisters, no DNA)"]
["Stage 2","3599_3","Female","SPX","Blood","Blood","European","6q25.3","6:155906594-157336808",1430215,"Gain","ARID1B","Paternal","qPCR","CNV also present in unaffected sister"]
["Stage 1","5386_3","Male","MPX","Blood","Blood","Other","6q25.3","6:156785155-158489874",1704720,"Loss","ARID1B, MIR3692, SERAC1, SNX9, SYNJ2, ZDHHC14","De novo","qPCR, Illumina 1M-duo for sib","1 brother with high functioning ASD (with none of the abnormalities present in his brother), no CNV"]
["Stage 1","6164_3","Female","SPX","UNK (blood or CL)","UNK (blood or CL)","European","6q25.3","6:160023074-160081618",58545,"Gain","SOD2, WTAP","De novo","qPCR","(1 healthy sister, no DNA)"]
["Stage 1","14270_3930","Female","SPX","Blood","Blood","European","6q25.3-q27","6:160773919-170761395",9987477,"Gain","10 Mb 6q25.3-q27 duplication (54 genes), chromosomal abnormality (unbalanced translocation)","De novo","FISH","(1 healthy sibling, not tested)","chromosomal abnormality, excluded from main analyses"]
["Stage 2","8612_201","Male","UNK","Blood","Blood","European","6q26","6:162588879-162629938",41060,"Loss","PARK2","De novo","qPCR","(not tested)"]
["Stage 2","8617_201","Male","UNK","Blood","Blood","European","6q26","6:162685572-162789187",103616,"Loss","PARK2","Maternal","qPCR","(not tested)"]
["Stage 2","8612_201","Male","UNK","Blood","Blood","European","6q26","6:162823171-162855421",32251,"Gain","PARK2 intronic","Paternal","qPCR","(not tested)"]
["Stage 2","8404_201","Male","MPX","Blood","Blood","European","6q27","6:169136788-170761395",1624608,"Loss","14 genes, including DLL1, PDCD2, PSMB1, TBP, TCTE3, THBS2 and WDR27","De novo","qPCR","(no siblings)"]
["Stage 2","8588_201","Male","UNK","Blood","Blood","European","7p21.3","7:10068058-10098695",30638,"Loss","—","Paternal","qPCR","(no siblings)"]
["Stage 1","5122_3","Male","MPX","CL","CL","European","7p21.1","7:17868378-18192733",324356,"Gain","HDAC9, PRPS1L1, SNX13","Maternal","qPCR, Illumina 1M-duo for sib","1 brother with autism, no CNV (1 non-ASD sister, not tested)"]
["Stage 1","3164_3","Male","MPX","CL","CL","European","7p21.1","7:18450792-18490822",40031,"Loss","HDAC9","Paternal","qPCR","1 brother with autism, no CNV"]
["Stage 2","9809_202","Male","SPX","Blood","Blood","Other","7p15.2","7:25040936-25095313",54378,"Gain","—","Maternal","qPCR","(not tested)"]
["Stage 2","6346_3","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","7p15.2","7:26249181-26363764",114584,"Loss","SNX10","Maternal","qPCR","(not tested)"]
["Stage 1","6127_3","Female","SPX","Blood","Blood","European","7p15.1","7:29175877-29503232",327356,"Gain","CHN2","Paternal","qPCR","(1 healthy sister, no DNA)"]
["Stage 2","3576_4","Male","UNK","Blood","Blood","European","7p14.1","7:38239830-38346971",107142,"Loss|cxLoss","TARP","De novo","qPCR","(not tested)"]
["Stage 2","18174_301","Male","SPX","CL","CL","European","7p12.1","7:53229450-53537639",308190,"Loss","—","Maternal","qPCR","(not tested)"]
["Stage 2","20006_1025001","Male","SPX","CL","CL","European","7p12.1","7:53428180-53557744",129565,"Loss","—","Paternal","qPCR","(not tested)"]
["Stage 2","6372_3","Male","SPX","Blood","Blood","European","7p11.2","7:55979255-55997714",18460,"Loss","MRPS17","Paternal","qPCR","(not tested)"]
["Stage 2","8446_201","Male","SPX","Blood","Blood","European","7q11.23","7:72344426-73782113",1437688,"Loss","Williams syndrome (7q11.23 deletion, 28 genes including ELN, GTF2I and GTF2IRD1)","De novo","qPCR","(not tested)"]
["Stage 2","18090_303","Male","MPX","CL","CL","Other","7q21.11","7:82971314-83021659",50346,"Loss","SEMA3E  intronic","Maternal","qPCR","no CNV in affected sib"]
["Stage 1","5200_3","Male","SPX","Blood","Blood","European","7q21.13","7:89626742-89825983",199242,"Gain","C7orf63, GTPBP10, STEAP1, STEAP2","Paternal","qPCR, Illumina 1M-duo for sib","1 non-ASD sister, no CNV"]
["Stage 1","1960_301","Female","MPX","CL","CL","European","7q22.1","7:102699832-102798745",98914,"Loss","DNAJC2, DPY19L2P2, PMPCB, PSMC2, SLC26A5","De novo","Illumina 550K (Glessner et al. 2009)","(not tested)"]
["Stage 1","3081_5","Female","MPX","CL","Buccal","Other","7q31.1","7:110835815-110867477",31663,"Loss","IMMP2L intronic","Maternal","LR-PCR","absent in 1 affected brother and 1 unaffected sister"]
["Stage 2","18178_302","Male","SPX","CL","CL","European","7q31.1","7:110835815-110987007",151193,"Loss","IMMP2L","Maternal","qPCR","(not tested)"]
["Stage 1","3320_003","Male","MPX","Buccal","Blood","European","7q31.1","7:110879714-110924988",45275,"Loss","IMMP2L","Paternal","qPCR","present in the unaffected sister, but absent in the brother with PDD-NOS"]
["Stage 1","6320_4","Male","SPX","Blood","Blood","European","7q35","7:145853798-145885593",31796,"Gain","CNTNAP2 intronic","Maternal","qPCR","(3 healthy sibs, no DNA)"]
["Stage 1","6266_3","Female","SPX","Blood","Blood","European","7q35","7:145853798-145885593",31796,"Gain","CNTNAP2 intronic","Maternal","qPCR","present in 1 brother with ADHD, absent in 1 healthy sister"]
["Stage 1","3018_3","Male","MPX","CL","CL","European","7q35","7:146059148-146251008",191861,"Gain","CNTNAP2","Maternal","qPCR","absent in 1 affected brother and 1 unaffected brother, present in 1 unaffected sister"]
["Stage 1","5014_4","Male","MPX","CL","CL","Other","7q36.2","7:153118877-153487764",368888,"Gain","DPP6","Paternal","qPCR","(1 brother with ASD, 1 non-ASD brother and 1 non-ASD sister, not tested)"]
["Stage 1","5130_3","Male","MPX","Blood","Blood","European","7q36.2","7:153742175-153788452",46278,"Loss","DPP6","Paternal","qPCR, Illumina 1M-duo for sib","present in 1 brother with ASD"]
["Stage 1","5370_3","Male","SPX","Blood","Blood","European","7q36.2","7:153775586-153844747",69162,"Loss","DPP6","De novo","qPCR, Affy 500K (Marshall et al. 2008), Agilent 1M","(no siblings)"]
["Stage 2","21020_1","Male","SPX","CL","Blood","European","8p23.1-p23.3","8:154984-6994825",6839842,"Loss","6.8 Mb 8p23.1-p23.3 deletion (27 genes), chromosomal abnormality (unbalanced translocation)","De novo","qPCR, FISH","(not tested)","chromosomal abnormality, excluded from main analyses"]
["Stage 1","5290_3","Male","SPX","Blood","Blood","Other","8p23.3","8:704383-1521910",817528,"Gain","DLGAP2, LOC286083","De novo","qPCR, Affy 500K (Marshall et al. 2008), Agilent 1M","1 brother with ASD features, no CNV by qPCR"]
["Stage 1","6010_4","Male","MPX","CL","CL","European","8p23.2","8:2334306-3290879",956574,"Gain","CSMD1","Paternal","qPCR","(not tested)"]
["Stage 1","2234_1","Male","SPX","Blood","Blood","Other","8p23.2","8:3773951-3780096",6146,"Loss","CSMD1 intronic","Maternal","qPCR","(not tested)"]
["Stage 1","3307_3","Male","MPX","Buccal","Buccal","European","8p23.1","8:6316818-6341678",24861,"Loss","MCPH1","Paternal","LR-PCR","also present in 1 unaffected brother, absent in 2 affected sisters"]
["Stage 1","5354_3","Female","SPX","Blood","Blood","European","8p23.1","8:10653990-10729568",75579,"Loss","MIR1322, PINX1","Paternal","qPCR, Illumina 1M-duo for sib","1 non-ASD sister, no CNV"]
["Stage 1","3048_3","Male","MPX","Buccal","Buccal","European","8p22","8:17007133-17015761",8629,"Loss","EFHA2","Maternal","LR-PCR","also present in sister with potential broader phenotype, absent in affected brother and absent from sister with unknown phenotype"]
["Stage 1","13137_1543","Female","SPX","Blood","Blood","European","8p11.1-q12.1","8:31928590-58996070",27067481,"Gain","Ring chromosome 8 syndrome (27 Mb duplication, 109 genes), chromosomal abnormality","De novo","karyotype","(no siblings)","chromosomal abnormality, excluded from main analyses"]
["Stage 1","1142_4","Female","MPX","CL","CL","European","8q11.21","8:48631388-48802529",171142,"Gain","KIAA0146","De novo","Affy 5.0 (Bucan et al. 2009) ","(not tested)"]
["Stage 1","6321_3","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","8q12.3-q13.1","8:65354366-66254869",900504,"Loss","BHLHE22, CYP7B1, LOC100130155, LOC401463, MIR124-2","De novo","qPCR","(2 healthy sisters, no DNA)"]
["Stage 1","14072_1250","Male","SPX","Blood","Blood","European","8q13.1","8:66140254-66753892",613639,"Loss","ARMC1, LOC286186, MTFR1","De novo","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","2236_1","Male","SPX","Blood","Blood","European","8q13.3","8:72378104-72380244",2141,"Loss","EYA1 intronic","Maternal","qPCR","(not tested)"]
["Stage 2","8500_201","Male","MPX","Blood","Blood","European","8q21.11","8:74692898-74967280",274383,"Loss","STAU2, UBE2W","De novo","qPCR","(not tested)"]
["Stage 2","8559_201","Female","SPX","Blood","Blood","European","8q21.13","8:82090958-83921979",1831022,"Loss","11 genes, including CHMP4C, PAG1, PMP2, SLC10A5, SNX16 and ZFAND1","Paternal","qPCR","(not tested)"]
["Stage 2","18116_302","Male","MPX","CL","CL","European","8q21.13","8:83693730-83806387",112658,"Gain","—","Unknown (not maternal, father no DNA)","qPCR","no CNV in affected sib"]
["Stage 2","3468_3","Male","SPX","Blood","Blood","European","8q21.2","8:86910517-86946730",36214,"Loss","—","Maternal","qPCR","(no siblings)"]
["Stage 2","20034_1229001","Male","SPX","Blood","Blood","European","8q21.3","8:89674652-89965640",290989,"Gain","—","Paternal","qPCR","(not tested)"]
["Stage 1","6240_4","Male","SPX","Blood","Blood","European","8q22.3","8:104451635-104607137",155503,"Loss","CTHRC1, DCAF13, RIMS2, SLC25A32","Paternal","qPCR","(1 healthy sister, not tested)"]
["Stage 1","3268_4","Male","MPX","CL","CL","European","8q24.11","8:118212477-118243899",31423,"Loss","SLC30A8","Paternal","LR-PCR","also present in affected brother and unaffected sister"]
["Stage 1","5032_4","Male","MPX","Blood","Blood","European","9p24.3","9:98998-334508",235511,"Loss","C9orf66, CBWD1, DOCK8, FOXD4","De novo","qPCR","1 sister with ASD, no CNV"]
["Stage 1","13123_1403","Female","UNK","Blood","Blood","European","9p24.2-p24.3","9:98998-3682923",3583926,"Loss","Terminal 9p deletion (14 genes)","De novo","qPCR","(not tested)"]
["Stage 1","2234_1","Male","SPX","Blood","Blood","Other","9p24.3","9:175632-422918",247287,"Gain","C9orf66, DOCK8","Maternal","qPCR, Affy 6.0","(not tested)"]
["Stage 1","1957_303","Female","MPX","CL","CL","European","9p24.3","9:243594-362341",118748,"Gain","DOCK8","Maternal","Illumina 550K (Glessner et al. 2009)","(not tested)"]
["Stage 1","5275_3","Female","SPX","Blood","Blood","Other","9p24.3","9:288719-676170",387452,"Gain","DOCK8, KANK1","Paternal","qPCR","(1 MZ twin with ASD, not tested)"]
["Stage 1","2238_1","Male","SPX","Blood","Blood","Other","9p24.3","9:600460-694075",93616,"Loss","KANK1","Paternal","qPCR, Affy 6.0","(not tested)"]
["Stage 1","6246_4","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","9p23","9:9399606-9631169",231564,"Loss","PTPRD","De novo","qPCR","absent in 1 healthy sister"]
["Stage 2","20128_4016001","Male","SPX","Blood","Blood","European","9p22.2","9:17586833-17617988",31156,"Gain","SH3GL2 intronic","Paternal","qPCR","(no siblings)"]
["Stage 1","3210_4","Male","MPX","CL","CL","European","9p21.3","9:23073305-23168368",95064,"Loss","—","Paternal","LR-PCR and sequencing","CNV absent in affected brother"]
["Stage 1","3019_3","Male","MPX","Buccal","Buccal","European","9q21.11-q21.12","9:72482886-73063512",580627,"Loss","MIR204, TRPM3","Paternal","qPCR, LR-PCR (sequencing coordinates: chr9:72480413-73064196, size: 583,784 bp), FISH (Pagnamenta et al. 2011, PMID: 21484199)","CNV present in affected brother and in healthy sister"]
["Stage 1","14026_510","Male","SPX","Blood","Blood","European","9q21.13","9:74970534-74977981",7448,"Gain","ANXA1","Maternal","qPCR","(not tested)"]
["Stage 1","14192_3160","Male","UNK","Blood","Blood","European","9q21.13","9:74970534-74977981",7448,"Gain","ANXA1","Maternal","qPCR","(not tested)"]
["Stage 1","14272_3950","Female","SPX","Blood","Blood","European","9q21.13","9:74971066-74977981",6916,"Gain","ANXA1","Paternal","qPCR","(not tested)"]
["Stage 2","16089_1571115001","Male","SPX","CL","CL","European","9q22.33","9:100940231-100952579",12349,"Loss","TGFBR1","Maternal","qPCR","(unaffected sibling not tested)"]
["Stage 1","14237_2650","Male","SPX","Blood","Blood","European","9q31.1","9:103456776-107140273",3683498,"Loss","16 genes, including ABCA1, CYLC2, GRIN3A, SLC44A1 and SMC2","De novo","qPCR","(not tested)"]
["Stage 2","14417_5260","Male","SPX","CL","CL","European","9q33.1","9:117311405-117727764",416360,"Loss","C9orf27","De novo","qPCR","(not tested)"]
["Stage 2","20115_1548001","Male","MPX","Blood","Blood","European","9q33.1","9:118916775-118967331",50557,"Loss","ASTN2 intronic","Paternal","qPCR","no CNV in affected sib"]
["Stage 1","14184_3020","Male","SPX","Blood","Blood","European","9q33.2","9:124209751-124398737",188987,"Gain","OR1J1, OR1J2, OR1J4, OR1L8, OR1N1, OR1N2","Maternal","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","14111_2000","Male","SPX","Blood","Blood","European","9q33.2","9:124209751-124398737",188987,"Gain","OR1J1, OR1J2, OR1J4, OR1L8, OR1N1, OR1N2","Paternal","qPCR","(1 healthy sister, no DNA)"]
["Stage 2","9756_201","Male","SPX","Blood","Blood","Other","9q34.12","9:132572435-132597937",25503,"Loss","ABL1","De novo","qPCR","(not tested)"]
["Stage 1","5136_4","Male","MPX","Blood","Blood","European","9q34.3","9:138753347-138762844",9498,"Loss","LCN10, LCN6, LOC100128593","Maternal","qPCR","(1 brother with ASD and 1 non-ASD half-sister, not tested)"]
["Stage 2","6259_3","Male","SPX","Blood","Blood","European","9q34.3","9:139523184-140273252",750069,"Loss","Kleefstra syndrome (9q34.3 deletion including EHMT1)","De novo","qPCR","(1 healthy sister, no DNA)","array failed QC, CNV validated"]
["Stage 2","8422_202","Male","UNK","Blood","Blood","European","10p15.3","10:1699803-1789598",89796,"Gain","ADARB2","Maternal","qPCR","(no siblings)"]
["Stage 1","3263_3","Male","MPX","Buccal","Buccal","European","10p15.2","10:3167320-3226016",58697,"Loss","LOC100507034, PFKP, PITRM1","Paternal","LR-PCR and sequencing","also present in affected brother (3263_004), absent in mother and unaffected sister"]
["Stage 2","18116_302","Male","MPX","CL","CL","European","10p11.23","10:29797497-31133591",1336095,"Gain","KIAA1462, LOC729668, LYZL2, MAP3K8, MIR604, MIR938, MTPAP, SVIL","Unknown (not maternal, father no DNA)","qPCR","no CNV in affected sib"]
["Stage 2","18172_302","Male","SPX","CL","CL","Other","10p11.21","10:34963905-35536952",573048,"Gain","CREM, CUL2, PARD3","De novo","qPCR","(1 unaffected dizygotic twin sister, not tested)"]
["Stage 1","5262_4","Male","SPX","CL","CL","European","10q11.21","10:42600836-43271395",670560,"Gain","BMS1, CSGALNACT2, FXYD4, HNRNPF, RASGEF1A, RET, ZNF487P","Paternal","qPCR, Illumina 1M-duo for sibs","1 non-ASD brother and 1 non-ASD sister, no CNV in either"]
["Stage 2","6301_3","Male","SPX","Blood","Blood","European","10q11.21","10:43056322-43140632",84311,"Gain","RASGEF1A","Maternal","qPCR","(no siblings)"]
["Stage 2","4312_1","Male","SPX","Blood","Blood","European","10q11.21-q11.23","10:45550419-51496386",5945968,"Loss","10q11.21-q11.23 deletion (56 genes)","Paternal","qPCR (Griswold et al. 2011, PMID: 21360829)","CNV present in 1 unaffected sister, absent in 1 non-ASD brother with ADHD and bipolar disorder"]
["Stage 2","8534_201","Male","SPX","Blood","Blood","European","10q11.21-q11.23","10:45633089-51564756",5931668,"Loss","10q11.21-q11.23 deletion (56 genes)","De novo","qPCR","(1 healthy brother and 1 healthy sister, not tested)"]
["Stage 2","9879_202","Male","SPX","Blood","Blood","Other","10q11.23","10:51166802-51263692",96891,"Gain","MSMB, NCOA4, TIMM23","Maternal","qPCR","(not tested)"]
["Stage 2","9882_202","Male","SPX","Blood","Blood","Other","10q21.1","10:57059346-57102512",43167,"Loss","—","Maternal","qPCR","(not tested)"]
["Stage 1","5349_3","Male","SPX","CL","CL","European","10q21.1","10:58409439-58421439",12001,"Gain","—","Paternal","qPCR","(1 non-ASD brother and 1 non-ASD sister, not tested)"]
["Stage 1","3209_004","Male","MPX","Buccal","Blood","European","10q21.3","10:66980652-66983475",2824,"Loss","—","Paternal","qPCR","present in sister with autism"]
["Stage 1","3311_3","Male","MPX","Buccal","Blood","European","10q21.3","10:67688367-67759307",70941,"Loss","CTNNA3","Maternal","LR-PCR","present in 1 brother with PDD-NOS, absent in 1 affected brother"]
["Stage 1","3209_4","Male","MPX","Buccal","Blood","European","10q21.3","10:67741619-67788456",46838,"Loss","CTNNA3 intronic","Paternal","LR-PCR","absent in 1 affected sibling"]
["Stage 1","3156_3","Male","MPX","Buccal","Blood","European","10q21.3","10:67741619-67788456",46838,"Loss","CTNNA3 intronic","Paternal","LR-PCR","absent in 1 sister with autism"]
["Stage 1","3321_3","Male","MPX","Buccal","Blood","European","10q21.3","10:67741619-67788456",46838,"Loss","CTNNA3 intronic","Maternal","LR-PCR","absent in 1 sister with autism"]
["Stage 1","3135_4","Male","MPX","Buccal","Blood","European","10q21.3","10:67748487-67785209",36723,"Loss","CTNNA3 intronic","Maternal","LR-PCR","absent in 1 affected brother and 1 socially awkward sister (no ASD diagnosis)"]
["Stage 1","3134_4","Male","MPX","Buccal","Blood","European","10q21.3","10:67838960-67885161",46202,"Loss","CTNNA3 intronic","Maternal","LR-PCR","present in 1 affected brother"]
["Stage 1","3093_4","Male","MPX","Buccal","Blood","European","10q21.3","10:67987089-68067310",80222,"Loss","CTNNA3","Maternal","LR-PCR","absent in 1 brother with autism"]
["Stage 1","3169_4","Male","MPX","Buccal","Blood","European","10q21.3","10:68029140-68183933",154794,"Loss","CTNNA3","Maternal","LR-PCR","also present in affected brother (3169_003)"]
["Stage 1","3034_3","Male","MPX","Buccal","Blood","European","10q21.3","10:68099569-68167094",67526,"Loss","CTNNA3 intronic","Paternal","LR-PCR","absent in 1 affected sibling"]
["Stage 2","14393_5020","Male","SPX","CL","CL","European","10q22.2","10:74801551-75278951",477401,"Loss","14 genes, including CAMK2G, CHCHD1, NDST2, SYNPO2L and ZMYND17","De novo","qPCR","(not tested)"]
["Stage 2","4446_1","Male","SPX","Blood","Blood","European","10q23.1","10:87754758-87839034",84277,"Loss","GRID1 intronic","Paternal","qPCR (Griswold et al. 2011, PMID: 21360829)","(not tested)"]
["Stage 2","6301_3","Male","SPX","Blood","Blood","European","10q26.2","10:128822743-128960575",137833,"Loss","DOCK1, FAM196A","Paternal","qPCR","(no siblings)"]
["Stage 1","5004_3","Male","MPX","Blood","Blood","European","10q26.3","10:134591133-134689210",98078,"Gain","C10orf93","Paternal","qPCR, Illumina 1M-duo for sib","present in 1 brother with autism"]
["Stage 1","5017_3","Male","MPX","CL","CL","European","10q26.3","10:135134088-135230489",96402,"Gain","CYP2E1, SPRNP1, SYCE1","Maternal","qPCR","(1 brother with autism, not tested)"]
["Stage 2","16072_1571036001","Male","SPX","CL","CL","European","11p15.5","11:381049-1019320",638272,"Gain","35 genes, including CHID1, DEAF1, HRAS, SLC25A22, and TSPAN4","Paternal","qPCR","(unaffected sibling not tested)"]
["Stage 1","5263_3","Male","SPX","Blood","Blood","Other","11p15.4","11:5397196-5454375",57180,"Gain","OR51B5, OR51I1, OR51I2, OR51Q1","Maternal","qPCR","(1 non-ASD brother with possible ADHD, not tested)"]
["Stage 2","21012_1","Male","SPX","CL","CL","European","11p15.4","11:6807877-6867703",59827,"Loss","OR10A2, OR10A4, OR10A5","Paternal","qPCR","(not tested)"]
["Stage 2","8404_201","Male","MPX","Blood","Blood","European","11q12.3","11:62603928-62867625",263698,"Loss","SLC22A10, SLC22A24, SLC22A25","Paternal","qPCR","(no siblings)"]
["Stage 2","6325_3","Male","SPX","Blood","Blood","European","11q13.3","11:70077507-70506315",428809,"Loss","MIR3664, SHANK2","De novo","qPCR","(no siblings)"]
["Stage 1","6319_3","Male","SPX","Blood","Blood","European","11q13.3","11:70119917-70187872",67956,"Loss","SHANK2","De novo","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","5237_3","Male","SPX","Blood","Blood","European","11q13.3","11:70154458-70220632",66175,"Loss","SHANK2","De novo","qPCR, Agilent 1M","1 non-ASD sister, no CNV"]
["Stage 2","20018_1102001","Male","SPX","Blood","Blood","European","11q14.1","11:81178281-81212713",34433,"Loss","—","Unknown (not maternal, father bad DNA)","qPCR","(not tested)"]
["Stage 2","8549_201","Male","UNK","Blood","Blood","European","11q14.2-q14.3","11:85944331-87925352",1981022,"Loss","CTSC, FZD4, GRM5, ME3, PRSS23, RAB38, TMEM135","Paternal","qPCR","(1 healthy sister, not tested)"]
["Stage 2","18178_302","Male","SPX","CL","CL","European","11q14.3","11:90279914-90314509",34596,"Loss","—","Maternal","qPCR","(not tested)"]
["Stage 2","8404_201","Male","MPX","Blood","Blood","European","11q21","11:96230931-96291346",60416,"Loss","—","Maternal","qPCR","(no siblings)"]
["Stage 1","6191_3","Male","MPX","UNK (blood or CL)","UNK (blood or CL)","European","11q22.1","11:98412813-98476682",63870,"Gain","CNTN5 intronic","Maternal","qPCR","absent in 1 unaffected sister (no DNA available for 1 brother with ID)"]
["Stage 2","8418_201","Male","UNK","Blood","Blood","European","11q22.3","11:107146021-107375709",229689,"Gain","RAB39, SLC35F2","Maternal","qPCR","(no siblings)"]
["Stage 1","5119_3","Female","MPX","CL","CL","Other","11q23.3","11:117452643-117537452",84810,"Gain","LOC100526771, SCN4B, TMPRSS4","Paternal","qPCR","(1 sister with autism, not tested)"]
["Stage 1","6240_4","Male","SPX","Blood","Blood","European","11q24.2-q25","11:126633939-132060374",5426436,"Loss","Jacobsen syndrome (11q deletion, 20 genes)","De novo","qPCR","absent in 1 healthy sister"]
["Stage 2","6185_5","Male","MPX","Blood","Blood","European","11q24.3-q25","11:130144888-131093755",948868,"Gain","NTM, SNX19","Paternal","qPCR","(no siblings)"]
["Stage 1","5136_4","Male","MPX","Blood","Blood","European","12p13.33","12:2115897-2127756",11860,"Loss","CACNA1C intronic","Paternal","qPCR","(1 brother with ASD and 1 non-ASD half-sister, not tested)"]
["Stage 1","5065_3","Male","MPX","Blood","Blood","European","12p13.33","12:2115897-2127756",11860,"Loss","CACNA1C intronic","Paternal","qPCR","(1 brother with autism, not tested)"]
["Stage 1","5004_3","Male","MPX","Blood","Blood","European","12p13.33","12:2115897-2127756",11860,"Loss","CACNA1C intronic","Maternal","qPCR, Illumina 1M-duo for sib","1 brother with autism, no CNV "]
["Stage 1","5269_3","Male","SPX","Blood","Blood","European","12p13.33","12:2115897-2127756",11860,"Loss","CACNA1C intronic","Paternal","qPCR, Illumina 1M-duo for sib","1 non-ASD brother, no CNV "]
["Stage 1","5106_3","Male","MPX","Blood","Blood","European","12p13.33","12:2115897-2127756",11860,"Loss","CACNA1C intronic","Maternal","qPCR","CNV present in 1 sister with autism (5106-4)"]
["Stage 1","5106_3","Male","MPX","Blood","Blood","European","12p13.32","12:3244089-3279231",35143,"Gain","TSPAN9","Paternal","qPCR, Affy 500K (Marshall et al. 2008), Illumina 1M-duo for sib","CNV present in 1 sister with autism (5106-4)"]
["Stage 1","5347_3","Male","SPX","CL","CL","European","12p13.31","12:9760538-9911534",150997,"Loss","CD69, CLEC2B, CLECL1, KLRF1","Paternal","qPCR","(1 non-ASD sister, not tested)"]
["Stage 1","13046_553","Male","UNK","Blood","Blood","European","12p13.2","12:11407199-11436086",28888,"Loss","PRB2","De novo","qPCR","(not tested)"]
["Stage 2","4176_1","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","12p13.1","12:13753741-13788728",34988,"Loss","GRIN2B intronic","Maternal","qPCR (Griswold et al. 2011, PMID: 21360829)","(not tested)"]
["Stage 1","2234_1","Male","SPX","Blood","Blood","Other","12q12","12:38587878-38603284",15407,"Loss","SLC2A13 intronic","Maternal","qPCR, Affy 6.0","(not tested)"]
["Stage 2","6177_3","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","12q12","12:39794750-39957915",163166,"Loss","PDZRN4","Unknown (not paternal, mother bad DNA)","qPCR","(no siblings)"]
["Stage 1","6053_3","Male","MPX","CL","UNK (blood or CL)","European","12q13.2-q14.1","12:54218922-58779615",4560694,"Gain","4.5 Mb 12q13 duplication (101 genes)","De novo","qPCR","absent in 1 sister with Asperger syndrome"]
["Stage 2","18091_301","Male","MPX","CL","CL","Other","12q21.2","12:75129049-75207987",78939,"Gain","—","Unknown (not maternal, father bad DNA)","qPCR","CNV also present in affected sib"]
["Stage 1","5272_3","Male","MPX","Blood","Blood","Other","12q23.1","12:98445422-98540678",95257,"Loss","ANKS1B intronic","De novo","qPCR, Agilent 1M, Illumina 1M-duo for sib","1 brother with autism, no CNV"]
["Stage 2","4374_1","Male","SPX","Blood","Blood","European","13q12.12","13:22409581-23826468",1416888,"Loss","9 genes, including MIPEP, SACS, SGCG, SPATA13 and TNFRSF19","Paternal","qPCR (Griswold et al. 2011, PMID: 21360829)","(not tested)"]
["Stage 2","6233_4","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","Other","13q12.12","13:22445855-23861016",1415162,"Gain","9 genes, including MIPEP, SACS, SGCG, SPATA13 and TNFRSF19","Maternal","qPCR","no CNV in unaffected sib"]
["Stage 1","3264_3","Male","MPX","CL","CL","European","13q21.1","13:52306405-52713799",407395,"Loss","OLFM4, PCDH8","Paternal","LR-PCR and sequencing","also present in affected brother (3264_004)"]
["Stage 1","13094_1113","Male","MPX","Blood","Blood","European","13q21.31","13:63231043-63277373",46331,"Gain","—","De novo","qPCR","(not tested)"]
["Stage 2","9879_202","Male","SPX","Blood","Blood","Other","13q34","13:113094274-113281796",187523,"Gain","ADPRHL1, DCUN1D2, TMCO3","Maternal","qPCR","(not tested)"]
["Stage 1","1050_3","Female","MPX","CL","CL","European","14q11.2","14:20279711-20345174",65464,"Gain","EDDM3A, EDDM3B, RNASE1, RNASE6","De novo","Illumina 550K (Glessner et al. 2009), Affy 5.0 (Bucan et al. 2009)","(not tested)"]
["Stage 2","3576_4","Male","UNK","Blood","Blood","European","14q11.2","14:21644569-21683530",38962,"Loss","—","Paternal","qPCR","(not tested)"]
["Stage 2","8638_201","Male","UNK","Blood","Blood","European","14q13.2","14:35203374-35369853",166480,"Loss","BRMS1L, RALGAPA1","De novo","qPCR","(not tested)"]
["Stage 1","3098_3","Male","MPX","CL","CL","European","14q21.3","14:44738955-44769172",30218,"Loss","FANCM, MIS18BP1","Maternal","LR-PCR and sequencing","CNV also present in affected brother, absent in unaffected brother"]
["Stage 2","4272_1","Male","SPX","Blood","Blood","European","14q23.2-q23.3","14:63824114-65347410",1523297,"Loss","18 genes, including AKAP5, CHURC1, ESR2, GPX2, HSPA2, RAB15 and ZBTB1 ","De novo","qPCR (Griswold et al. 2011, PMID: 21360829)","not present in 2 unaffected sibs"]
["Stage 1","6362_3","Male","SPX","UNK (blood or CL)","Blood","European","14q31.1","14:78536692-78578318",41627,"Loss","NRXN3 intronic","Paternal","qPCR","(1 healthy paternal half-sister, no DNA)"]
["Stage 1","2230_1","Male","SPX","Blood","Blood","European","14q31.1","14:78557401-78589854",32454,"Loss","NRXN3 intronic","Paternal","qPCR, Affy 6.0","(not tested)"]
["Stage 2","17009_1","Male","SPX","CL","CL","European","14q31.1","14:78575296-78596793",21498,"Loss","NRXN3 intronic","De novo","qPCR","(not tested)"]
["Stage 2","8514_202","Male","MPX","Blood","Blood","European","14q32.2","14:99945019-100126033",181015,"Gain","BEGAIN, WDR25","Maternal","qPCR","(not tested)"]
["Stage 2","8117_202","Male","MPX","Blood","Blood","European","15q11.2","15:18560401-20778963",2218563,"Loss","15q11.2 microdeletion BP1-BP2 (20 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","Maternal","qPCR","CNV absent in unaffected sib"]
["Stage 2","8430_204","Male","SPX","Blood","Blood","Other","15q11.2","15:20301669-20777695",476027,"Loss","15q11.2 microdeletion BP1-BP2 (5 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","De novo","qPCR","de novo CNV in affected MZ twin, no CNV in unaffected sibling"]
["Stage 2","2288_1","Male","SPX","Blood","Blood","European","15q11.2","15:20301669-20777695",476027,"Loss","15q11.2 microdeletion BP1-BP2 (5 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","Maternal","qPCR","(not tested)"]
["Stage 1","6319_3","Male","SPX","Blood","Blood","European","15q11.2","15:20305097-20773130",468034,"Loss","15q11.2 microdeletion BP1-BP2 (5 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","Paternal","MLPA","(1 healthy brother, no DNA)"]
["Stage 1","5453_4","Male","MPX","Blood","Blood","European","15q11.2","15:20303106-20836955",533850,"Loss","15q11.2 microdeletion BP1-BP2 (7 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","Paternal","qPCR, Agilent 1M, Illumina 1M-duo for sibs","2 non-ASD brothers, no CNV"]
["Stage 1","1987_301","Male","MPX","CL","CL","European","15q11.2","15:20090262-21038099",947838,"Gain","15q11.2 microduplication BP1-BP2 (11 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","Maternal","Illumina 550K (Glessner et al. 2009)","(not tested)"]
["Stage 2","9759_201","Female","UNK","Blood","Blood","European","15q11.2","15:19777876-20778963",1001088,"Gain","15q11.2 microduplication BP1-BP2 (12 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","De novo","qPCR","(not tested)"]
["Stage 2","6248_3","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","15q11.2","15:20301669-20796527",494859,"Gain","15q11.2 microduplication BP1-BP2 (5 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","Paternal","MLPA","(2 brothers, no DNA)"]
["Stage 1","5250_4","Male","MPX","CL","Blood","European","15q11.2","15:20303106-20800564",497459,"Gain","15q11.2 microduplication BP1-BP2 (5 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","Paternal","qPCR, Illumina 1M-duo for sib","present in 1 brother with ASD (5250_3)"]
["Stage 1","5263_3","Male","SPX","Blood","Blood","Other","15q11.2","15:20235613-20807351",571739,"Gain","15q11.2 microduplication BP1-BP2 (8 genes, including CYFIP1, NIPA1, NIPA2 and TUBGCP5)","Maternal","qPCR","(1 non-ASD brother with possible ADHD, not tested)"]
["Stage 2","8117_202","Male","MPX","Blood","Blood","European","15q11.2-q13.1","15:21168391-26217954",5049564,"Gain","15q11-q13 duplication syndrome (101 genes, including UBE3A)","Maternal","qPCR","CNV also present in affected sib, absent in unaffected brother"]
["Stage 1","13050_593","Male","UNK","Blood","Blood","European","15q11.2-q13.1","15:21190624-26203954",5013331,"Gain","15q11-q13 duplication syndrome (101 genes, including UBE3A)","De novo","qPCR","(not tested)"]
["Stage 2","8741_201","Female","MPX","Blood","Blood","Other","15q11.2-q13.1","15:21168391-26315093",5146703,"Gain","15q11-q13 duplication syndrome (103 genes, including UBE3A)","Maternal","qPCR","duplication present in brother with autism and in 1 sister with speech delay; absent in 3 healthy sisters"]
["Stage 2","17035_1","Female","SPX","Blood","Blood","European","15q11.2-q13.1","15:20274130-26120360",5846231,"Gain","15q11-q13 duplication syndrome (111 genes, including UBE3A)","De novo","qPCR","(not tested)"]
["Stage 2","20069_1328001","Male","SPX","Blood","Blood","European","15q11.2-q13.1","15:20203578-26209270",6005693,"Gain","15q11-q13 duplication syndrome (112 genes, including UBE3A)","De novo","qPCR","(no siblings)"]
["Stage 2","8630_201","Male","MPX","Blood","Blood","European","15q11.2-q13.1","15:19800798-26209270",6408473,"Gain","15q11-q13 duplication syndrome (117 genes, including UBE3A)","De novo","qPCR","(no siblings)"]
["Stage 2","20187_1464001","Male","SPX","Blood","Blood","European","15q11.2-q13.1","15:18811937-26209270",7397334,"Gain","15q11-q13 duplication syndrome (125 genes, including UBE3A)","De novo","qPCR","(no siblings)"]
["Stage 1","13043_523","Male","UNK","Blood","Blood","European","15q11.2","15:21914925-22008680",93756,"Gain","PWRN2","Both parents","qPCR","(1 healthy sister and 2 healthy DZ twin brothers, no DNA)"]
["Stage 1","1950_301","Male","MPX","CL","CL","European","15q13.1-q13.3","15:26762141-30436163",3674023,"Loss","15q13.3 deletion syndrome (22 genes, including CHRNA7)","Maternal","Illumina 550K (Glessner et al. 2009)","(not tested)"]
["Stage 2","16040_1571029001","Male","MPX","CL","CL","European","15q13.2-q13.3","15:28450423-30303265",1852843,"Loss","15q13.3 deletion syndrome (12 genes, including CHRNA7)","De novo","qPCR","(sib PDD-NOS, not tested)"]
["Stage 1","14167_2720","Male","SPX","Blood","Blood","European","15q13.2-q13.3","15:28705540-30436163",1730624,"Loss","15q13.3 deletion syndrome (9 genes, including CHRNA7)","Paternal","qPCR","(no siblings)"]
["Stage 2","18100_302","Male","MPX","CL","CL","European","15q13.2-q13.3","15:28714502-30303265",1588764,"Loss","15q13.3 deletion syndrome (9 genes, including CHRNA7)","Paternal","qPCR","CNV also present in brother and sister with autism"]
["Stage 1","5225_3","Male","SPX","Blood","Blood","European","15q13.1-q13.2","15:26887815-28157206",1269392,"Gain","APBA2, FAM189A1, LOC646278, NDNL2, TJP1","Paternal","qPCR, Agilent 1M, Illumina 1M-duo for sibs","present in 1 unaffected brother (5225_4) and 1 sister with mild cerebral palsy (5225_5)"]
["Stage 1","1231_3","Male","MPX","CL","CL","European","15q13.2","15:28187888-28881771",693884,"Loss","8 genes, including ARHGAP11B, CHRFAM7A, DKFZP434L187 and FAM7A1","Paternal","Illumina 550K (Glessner et al. 2009)","(not tested)"]
["Stage 2","6325_3","Male","SPX","Blood","Blood","European","15q13.3","15:29792536-30303265",510730,"Gain","CHRNA7","Maternal","qPCR","(no siblings)"]
["Stage 2","6396_3","Male","MPX","UNK (blood or CL)","UNK (blood or CL)","European","15q13.3","15:29792640-30286443",493804,"Gain","CHRNA7","Paternal","qPCR","(no siblings)"]
["Stage 1","2236_1","Male","SPX","Blood","Blood","European","15q14","15:32459510-32606592",147083,"Loss","GOLGA8A, GOLGA8B, MIR1233-1, MIR1233-2","Maternal","qPCR, Affy 6.0","(not tested)"]
["Stage 1","5114_3","Male","MPX","CL","CL","European","15q15.3","15:42350178-42386578",36401,"Loss","CASC4","Maternal","qPCR","1 brother with autism, no CNV"]
["Stage 1","1956_302","Male","MPX","CL","CL","European","15q22.31","15:63073899-63183826",109928,"Gain","KBTBD13, LOC390595, MTFMT, OSTBETA, RASL12","Paternal","Illumina 550K (Glessner et al. 2009)","(not tested)"]
["Stage 1","6101_4","Male","MPX","UNK (blood or CL)","UNK (blood or CL)","Other","15q24.3","15:74735339-74929817",194479,"Loss","SCAPER","De novo","qPCR","absent in 1 brother with autism and 1 unaffected sister"]
["Stage 2","8695_201","Male","SPX","Blood","Blood","European","15q25.2","15:81728085-82623936",895852,"Loss","ADAMTSL3, BNC1, LOC648809, SH3GL3","De novo","qPCR","(not tested)"]
["Stage 2","5537_3","Male","MPX","CL","CL","European","15q25.2-q25.3","15:82722026-83529838",807813,"Loss","Distal 15q25.2 deletion syndrome (13 genes)","Maternal","Affy 500K, Illumina 2.5M, qPCR","1 sister (#61018) without social concerns without DEL, 1 brother (#61114) with ADHD and autism with DEL"]
["Stage 1","14181_2940","Male","SPX","Blood","Blood","European","15q25.2","15:82906265-82985247",78983,"Gain","LOC100506874, SCAND2, UBE2Q2P1, ZSCAN2","De novo","qPCR","(1 healthy sibling not tested)"]
["Stage 1","14070_1230","Male","MPX","Blood","Blood","European","15q26.1","15:91200007-91283004",82998,"Loss","CHD2, LOC100507217, MIR3175","De novo","qPCR","deletion present in brother with autism, ID and epilepsy"]
["Stage 2","8534_201","Male","SPX","Blood","Blood","European","15q26.1","15:91951725-92043989",92265,"Loss","—","Paternal","qPCR","(1 healthy brother and 1 healthy sister, not tested)"]
["Stage 2","16058_1571037001","Male","MPX","CL","CL","European","16p13.3","16:2051231-2079696",28466,"Gain","PKD1, TSC2","Paternal","qPCR","(brother with autism and 2 unaffected sisters, not tested)"]
["Stage 2","4182_1","Male","SPX","Blood","Blood","European","16p13.2","16:6866262-7042998",176737,"Loss","RBFOX1","Paternal","qPCR (Griswold et al. 2011, PMID: 21360829)","(not tested)"]
["Stage 2","4210_1","Male","SPX","Blood","Blood","European","16p13.2","16:6866262-7042998",176737,"Loss","RBFOX1","Paternal","qPCR (Griswold et al. 2011, PMID: 21360829)","(not tested)"]
["Stage 2","4461_1","Male","MPX","Blood","Blood","European","16p13.2","16:6866262-7042998",176737,"Loss","RBFOX1","Maternal","qPCR (Griswold et al. 2011, PMID: 21360829)","(not tested)"]
["Stage 2","4518_1","Male","SPX","Blood","Blood","European","16p13.2","16:6866262-7042998",176737,"Loss","RBFOX1","Paternal","qPCR (Griswold et al. 2011, PMID: 21360829)","(not tested)"]
["Stage 1","5208_3","Male","MPX","Blood","Blood","European","16p13.2","16:8636625-8714816",78192,"Gain","ABAT, METTL22","Paternal","qPCR, Illumina 1M-duo for sib","1 brother with autism, no CNV "]
["Stage 1","14283_4060 ","Male","SPX","Blood","Blood","European","16p13.11","16:14771033-16307313",1536281,"Loss","16p13.11 deletion syndrome (25 genes, including MYH11 and NDE1)","Maternal","qPCR","(1 sister with learning disabilities, not tested)"]
["Stage 2","20070_1331001","Male","SPX","Blood","Blood","European","16p13.11","16:14808871-15935225",1126355,"Gain","16p13.11 duplication (22 genes, including MYH11 and NDE1)","Maternal","qPCR","(not tested)"]
["Stage 2","3441_3","Male","SPX","Blood","Blood","European","16p13.11","16:14808871-16215852",1406982,"Loss","16p13.11 deletion syndrome (24 genes, including MYH11 and NDE1)","Paternal","qPCR","(not tested)"]
["Stage 2","14412_5210","Male","SPX","CL","CL","European","16p13.11","16:14960247-16307313",1347067,"Loss","16p13.11 deletion syndrome (19 genes, including MYH11 and NDE1)","Maternal","qPCR, LR-PCR","(1 healthy sibling, not tested)"]
["Stage 2","9766_202","Male","SPX","Blood","Blood","Other","16p13.11","16:15032942-16199484",1166543,"Gain","16p13.11 duplication (13 genes, including MYH11 and NDE1)","Maternal","qPCR","(no siblings)"]
["Stage 1","14142_2400","Male","SPX","Blood","Blood","European","16p13.11","16:15387380-16256106",868727,"Gain","16p13.11 duplication (10 genes, including MYH11 and NDE1)","Paternal","qPCR","(no siblings)"]
["Stage 1","5258_3","Male","SPX","Blood","Blood","European","16p13.11","16:15387380-16270740",883361,"Gain","16p13.11 duplication (10 genes, including MYH11 and NDE1)","Paternal","qPCR, Illumina 1M-duo for sib","1 non-ASD paternal half-sister, no CNV"]
["Stage 2","2265_1","Male","SPX","Blood","Blood","European","16p12.3-p13.11","16:15387380-18176669",2789290,"Gain","16p13.11 duplication (18 genes, including MYH11 and NDE1)","Maternal","qPCR","(3 unaffected half-siblings, 1 maternal and 2 paternal, no DNA)"]
["Stage 2","8549_201","Male","UNK","Blood","Blood","European","16p12.2","16:21509275-21647775",138501,"Loss","IGSF6, METTL9, OTOA","De novo","qPCR","(1 healthy sister, not tested)"]
["Stage 1","14071_1240","Male","SPX","Blood","Blood","European","16p12.1","16:21788416-22351124",562709,"Loss","C16orf52, CDR2, EEF2K, PDZD9, POLR3E, RRN3P3, UQCRC2, VWA3A","Paternal","qPCR","(not tested)"]
["Stage 1","6261_3","Male","SPX","Blood","Blood","European","16p12.1","16:21854731-22331199",476469,"Loss","C16orf52, CDR2, EEF2K, PDZD9, POLR3E, UQCRC2, VWA3A","Maternal","qPCR","(2 healthy sibs, no DNA)"]
["Stage 1","3174_3","Male","MPX","Buccal","Blood","European","16p12.1","16:21854731-22343312",488582,"Loss","C16orf52, CDR2, EEF2K, PDZD9, POLR3E, RRN3P3, UQCRC2, VWA3A","Paternal","qPCR, Agilent 1M","present in 1 brother with autism"]
["Stage 1","5382_3","Male","SPX","Blood","Blood","European","16p11.2","16:28730274-28950951",220678,"Gain","Distal 16p11.2 duplication (9 genes, including SH2B1)","Maternal","qPCR","CNV also present in unaffected sib "]
["Stage 2","2204_1","Male","SPX","Blood","Blood","European","16p11.2","16:29466569-30147029",680461,"Loss","16p11.2 deletion syndrome (42 genes, including MAPK3 and TBX6)","De novo","qPCR","(3 unaffected paternal half-siblings, no DNA)"]
["Stage 2","20089_1391001","Male","SPX","Blood","Blood","European","16p11.2","16:29502984-30107306",604323,"Loss","16p11.2 deletion syndrome (29 genes, including MAPK3 and TBX6)","De novo","qPCR","(unaffected younger dizygotic twins, not tested) "]
["Stage 1","5068_3","Female","MPX","Blood","Blood","European","16p11.2","16:29502984-30127026",624043,"Loss","16p11.2 deletion syndrome (40 genes, including MAPK3 and TBX6)","De novo","qPCR, Affy 500K (Marshall et al. 2008), Agilent 1M","1 brother with ASD, no CNV"]
["Stage 1","3211_3","Male","MPX","Buccal","Blood","European","16p11.2","16:29502984-30127026",624043,"Gain","16p11.2 duplication syndrome (40 genes, including MAPK3 and TBX6)","Maternal","qPCR","absent in 1 affected brother"]
["Stage 1","5262_4","Male","SPX","CL","CL","European","16p11.2","16:29502984-30210849",707866,"Gain","16p11.2 duplication syndrome (43 genes, including MAPK3 and TBX6)","De novo","qPCR, Affy 500K (Marshall et al. 2008)","1 non-ASD brother and 1 non-ASD sister, no CNV in either"]
["Stage 2","4030_1","Male","MPX","Blood","Blood","European","16p11.2","16:29554843-30107306",552464,"Gain","16p11.2 duplication syndrome (28 genes, including MAPK3 and TBX6)","De novo","qPCR (Griswold et al. 2011, PMID: 21360829)","not present in affected sib"]
["Stage 2","20127_4014001","Male","SPX","CL","CL","European","16p11.2","16:29554843-30130862",576020,"Loss","16p11.2 deletion syndrome (39 genes, including MAPK3 and TBX6)","Paternal","qPCR","(no siblings)"]
["Stage 1","5359_4","Male","SPX","Blood","Blood","European","16p11.2","16:29554843-30195224",640382,"Loss","16p11.2 deletion syndrome (42 genes, including MAPK3 and TBX6)","De novo","qPCR, Affy 500K (Marshall et al. 2008), Agilent 1M","1 non-ASD sister, no CNV"]
["Stage 1","3099_8","Male","MPX","CL","CL","European","16q21","16:60027157-61668976",1641820,"Loss","CDH8","Maternal","LR-PCR (sequencing coordinates: chr16:60025584-61667839, size: 1,642,256 bp) (Pagnamenta et al. 2011, PMID: 20972252)","present in 2 other affected brothers but not in 4 unaffected siblings"]
["Stage 1","5208_3","Male","MPX","Blood","Blood","European","16q23.1","16:74997300-75007489",10190,"Loss","CNTNAP4 intronic","Maternal","qPCR, Illumina 1M-duo for sib","1 brother with autism, no CNV"]
["Stage 2","20042_1249001","Male","SPX","Blood","Blood","European","16q23.1","16:75807900-75839129",31230,"Loss","—","Maternal","qPCR","(not tested)"]
["Stage 1","6356_5","Male","SPX","UNK (blood or CL)","Blood","European","16q24.1","16:82800294-82887663",87370,"Loss","KCNG4, WFDC1","Maternal","qPCR","(2 healthy sibs, no DNA)"]
["Stage 2","8703_201","Male","SPX","Blood","Blood","European","17p13.3","17:1092256-1249222",156967,"Gain","BHLHA9, TUSC5, YWHAE","Paternal","qPCR","no CNV in unaffected sib"]
["Stage 2","6413_4","Male","SPX","Blood","Blood","European","17p13.3","17:1621877-1631703",9827,"Gain","SERPINF1, SMYD4","Maternal","qPCR","no CNV in unaffected sib"]
["Stage 2","2271_1","Male","SPX","Blood","Blood","European","17p12","17:14040467-15435991",1395525,"Loss","Hereditary neuropathy with liability to pressure palsies (17p12 deletion, 11 genes including PMP22)","Maternal","qPCR","(no siblings)"]
["Stage 2","3439_3","Male","SPX","Blood","Blood","European","17p11.2","17:17156307-18262979",1106673,"Loss","Smith-Magenis syndrome (17p11.2 deletion, 22 genes including RAI1)","De novo","qPCR","no CNV in unaffected sister"]
["Stage 2","2211_1","Female","SPX","Blood","Blood","European","17p11.2","17:17169258-20101517",2932260,"Loss","Smith-Magenis syndrome (17p11.2 deletion, 53 genes including RAI1)","De novo","qPCR","(2 unaffected siblings, no DNA)"]
["Stage 2","14315_4320","Male","SPX","Blood","Blood","European","17q12","17:31621634-33323919",1702286,"Gain","17q12 duplication syndrome (24 genes, including ACACA, HNF1B and LHX1)","Maternal","qPCR","(older brother with language and motor delay, no DNA)"]
["Stage 2","8433_202","Male","MPX","Blood","Blood","European","17q12","17:33117766-33139608",21843,"Gain","HNF1B","Paternal","qPCR","duplication in brother with ASD, absent in unaffected sister"]
["Stage 1","5056_4","Male","MPX","Blood","Blood","European","17q12","17:34612208-34732327",120120,"Gain","FBXL20, RPL19, STAC2","De novo","qPCR, Illumina 1M-duo for sibs","1 brother with autism (5056_3), no CNV; 3 other non-ASD brothers: 5056_5, CNV (could be mosaic); 5056_6, CNV; 5056_7, no CNV"]
["Stage 2","8463_202","Male","MPX","Blood","Blood","European","17q22","17:52774693-52887687",112995,"Loss","MSI2","De novo","qPCR","no CNV in sib with PDD"]
["Stage 2","6109_3","Female","SPX","Blood","Blood","European","17q23.3","17:59404245-59430241",25997,"Gain","C17orf72","Maternal","qPCR","no CNV in unaffected sib"]
["Stage 1","6261_3","Male","SPX","Blood","Blood","European","17q24.2","17:61650712-61824330",173619,"Gain","APOH, PRKCA","Paternal","qPCR","(2 healthy sibs, no DNA)"]
["Stage 1","1165_3","Male","MPX","CL","CL","European","17q25.1","17:69345596-70202513",856918,"Gain","16 genes, including BTBD17, GPR142, GPRC5C, RAB37, RPL38 and TTYH2","Paternal","Illumina 550K (Glessner et al. 2009)","(not tested)"]
["Stage 2","9801_202","Male","SPX","Blood","Blood","Other","17q25.1","17:70791219-70870865",79647,"Gain","GRB2, SLC25A19","Paternal","qPCR","(not tested)"]
["Stage 1","5444_3","Male","SPX","Blood","Blood","European","17q25.3","17:76953064-77782267",829204,"Gain","38 genes, including ACTG1, DCXR, GPS1, LRRC45, SIRT7 and SLC16A3","De novo","qPCR, Affy 500K (Marshall et al. 2008), Agilent 1M, FISH","1 non-ASD sister, no CNV"]
["Stage 1","6164_3","Female","SPX","UNK (blood or CL)","UNK (blood or CL)","European","17q25.3","17:77760278-77802222",41945,"Gain","CCDC57, CSNK1D, SLC16A3","Maternal","qPCR","(1 healthy sister, no DNA)"]
["Stage 1","5444_3","Male","SPX","Blood","Blood","European","17q25.3","17:77785939-77849717",63779,"Loss","CSNK1D, SLC16A3","De novo","qPCR, Agilent 1M","1 non-ASD sister, no CNV"]
["Stage 1","3435_003","Female","SPX","Blood","Blood","European","18p11.21","18:11957792-12120394",162603,"Loss","IMPA2","Paternal","qPCR","present in an unaffected sister"]
["Stage 2","3477_3","Male","SPX","Blood","Blood","European","18q12.1","18:30280260-30327512",47253,"Loss","DTNA","De novo","qPCR","absent in unaffected brother"]
["Stage 1","14049_850","Male","SPX","Blood","Blood","European","18q12.2","18:35205049-35299318",94270,"Loss","LOC647946","Maternal","qPCR","(1 healthy sister, 1 healthy brother, no DNA)"]
["Stage 1","14262_3850","Male","SPX","Blood","Blood","European","18q12.2","18:35205049-35299318",94270,"Loss","LOC647946","Paternal","qPCR","(no siblings)"]
["Stage 2","18168_302","Male","SPX","CL","CL","European","18q21.32","18:56418823-56461584",42762,"Gain","—","Paternal","qPCR","no affected sib"]
["Stage 1","14058_1000","Male","MPX","Blood","Blood","European","18q22.3","18:69788042-70538070",750029,"Gain","9 genes, including CNDP1, CNDP2, CYB5A, FAM69C, FBXO15 and ZNF407","Maternal","qPCR","(not tested)"]
["Stage 2","14331_4450","Male","SPX","Blood","Blood","European","18q23","18:72085223-73670156",1584934,"Loss","GALR1, LOC284276, MBP, ZNF236, ZNF516","De novo","qPCR","(2 healthy brothers, not tested)"]
["Stage 1","6358_6","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","19p13.3","19:4548413-5287389",738977,"Loss","12 genes, including DPP9, FEM1A, PTPRS, TICAM1 and TNFAIP8L1","De novo","qPCR","(3 healthy sibs, no DNA)"]
["Stage 2","14391_5000","Male","SPX","CL","CL","European","19p13.2","19:12361149-12393330",32182,"Loss","ZNF799","Paternal","qPCR","(no siblings)"]
["Stage 1","3318_3","Male","MPX","Buccal","Buccal","European","19q13.11","19:38012308-38087253",74946,"Loss","CEP89, SLC7A9","Maternal","LR-PCR and sequencing","absent in affected brother"]
["Stage 1","5108_3","Male","MPX","CL","CL","European","19q13.32","19:52318905-52334620",15716,"Gain","SAE1","Paternal","qPCR","(1 brother with autism, not tested)"]
["Stage 1","3181_7","Male","MPX","CL","CL","European","19q13.32","19:52467295-52645983",178689,"Loss","C5AR1, DHX34, GPR77, MEIS3, PRR24, SLC8A2","Maternal","LR-PCR","no siblings; CNV absent in affected cousin and unaffected cousin (females)"]
["Stage 2","16097_1571153001","Male","SPX","CL","CL","European","19q13.32","19:52989040-53098186",109147,"Loss","CRX, SULT2A1, TPRX1","Maternal","qPCR","(brother with ADHD not tested)"]
["Stage 1","5340_3","Male","UNK","CL","CL","European","19q13.33","19:55873117-55929311",56195,"Loss","CLEC11A, SHANK1","Maternal","qPCR","(not tested)"]
["Stage 1","3222_4","Female","MPX","CL","CL","European","19q13.41","19:58580438-58602724",22287,"Loss","ZNF525, ZNF765","Paternal","LR-PCR","also present in affected sister"]
["Stage 1","5046_3","Male","MPX","CL","CL","Other","20p12.3","20:8607242-8637441",30200,"Loss","PLCB1","De novo","qPCR","1 brother with ASD, no CNV"]
["Stage 1","5335_3","Male","SPX","CL","CL","European","20p12.1","20:14545734-14948785",403052,"Loss","MACROD2, MACROD2-AS1","De novo","qPCR, Agilent 1M","(1 healthy sib, not tested)"]
["Stage 1","5250_4","Male","MPX","CL","Blood","European","20p12.1","20:14729684-14773787",44104,"Loss","MACROD2 intronic","Paternal","qPCR","(1 brother with ASD, not tested)"]
["Stage 1","5244_3","Male","SPX","Blood","Blood","European","20p12.1","20:14778453-14888687",110235,"Loss","MACROD2 intronic, MACROD2-AS1","Paternal","qPCR, Illumina 1M-duo for sibs","present in 1 non-ASD brother; 1 non-ASD sister, no CNV"]
["Stage 1","5066_4","Male","MPX","CL","Blood","Other","20p12.1","20:14818398-14879494",61097,"Loss","MACROD2 intronic, MACROD2-AS1","Maternal","qPCR","(1 brother with autism and 1 non-ASD brother, not tested)"]
["Stage 1","5061_3","Male","MPX","Blood","Blood","European","20p12.1","20:14820313-14879494",59182,"Loss","MACROD2 intronic, MACROD2-AS1","Maternal","qPCR, Illumina 1M-duo for sibs","1 brother with ASD and 1 with autism, no CNV in either"]
["Stage 1","6023_3","Male","MPX","UNK (blood or CL)","UNK (blood or CL)","European","20p12.1","20:14948785-15161293",212509,"Loss","MACROD2","Maternal","qPCR","present in 1 brother with PDD-NOS"]
["Stage 1","5021_5","Male","MPX","CL","CL","Other","20p12.1","20:14999717-15091806",92090,"Loss","MACROD2 intronic","Paternal","qPCR","(1 non-ASD brother and 1 sister with autism, not tested)"]
["Stage 1","3038_3","Male","MPX","CL","CL","European","20p11.23","20:17964236-18003164",38929,"Loss","OVOL2","Maternal","LR-PCR","no CNV in affected brother"]
["Stage 2","18113_302","Female","MPX","CL","CL","European","20p11.23","20:18109337-18444123",334787,"Gain","C20orf12, CSRP2BP, MGC44328, MIR3192, POLR3F, RBBP9, SEC23B, ZNF133","Paternal","qPCR","CNV also present in 2 affected sibs"]
["Stage 1","5420_3","Male","SPX","CL","CL","European","21p11.1-q22.3","21:1-247249719",247249719,"Gain","Down syndrome","De novo","karyotype","(1 non-ASD brother, not tested)","chromosomal abnormality, excluded from main analyses"]
["Stage 2","20180_1704001","Male","SPX","Blood","Blood","European","21q22.3","21:43018846-43444308",425463,"Gain","CBS, NDUFV3, PDE9A, PKNOX1, U2AF1, WDR4","De novo","qPCR","(not tested)"]
["Stage 1","2230_1","Male","SPX","Blood","Blood","European","22q11.1","22:15641026-15653178",12153,"Loss","XKR3","Paternal","qPCR, Affy 6.0","(not tested)"]
["Stage 1","3183_7","Male","MPX","Buccal","Buccal","European","22q11.21","22:17241748-19819918",2578171,"Loss","22q11.2 deletion syndrome (DiGeorge/velocardiofacial syndrome, 63 genes including TBX1)","De novo","qPCR","absent in 1 first degree cousin with autism"]
["Stage 2","8627_201","Male","SPX","Blood","Blood","European","22q11.21","22:17257787-19793730",2535944,"Gain","22q11.2 duplication syndrome (63 genes including TBX1)","De novo","qPCR","(2 healthy brothers, not tested)"]
["Stage 1","3127_4","Male","MPX","CL","CL","European","22q11.21","22:17257787-19793730",2535944,"Gain","22q11.2 duplication syndrome (63 genes including TBX1)","Paternal","qPCR","present in 1 affected brother"]
["Stage 2","16074_1571042001","Male","SPX","CL","CL","European","22q11.21","22:17257787-19793730",2535944,"Gain","22q11.2 duplication syndrome (63 genes including TBX1)","Paternal","qPCR","(sib ADHD not tested)"]
["Stage 1","5261_4","Female","MPX","Blood","Blood","European","22q11.21","22:17257787-19795780",2537994,"Gain","22q11.2 duplication syndrome (63 genes including TBX1)","Paternal","qPCR, Illumina 1M-duo for sibs","1 maternal half-brother with autism and 1 non-ASD sister; no CNV in either"]
["Stage 2","17015_1","Male","SPX","CL","CL","European","22q11.21","22:17257787-19795780",2537994,"Loss","22q11.2 deletion syndrome (DiGeorge/velocardiofacial syndrome, 63 genes including TBX1)","De novo","qPCR","(not tested)"]
["Stage 2","4271_1","Male","SPX","Blood","Blood","European","22q11.21","22:17257787-19795780",2537994,"Gain","22q11.2 duplication syndrome (63 genes including TBX1)","De novo","qPCR (Griswold et al. 2011, PMID: 21360829)","not present in unaffected sib"]
["Stage 1","6125_4","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","22q11.21","22:19051464-19793730",742267,"Gain","20 genes, including MED15, SCARF2, SERPIND1, SLC7A4, SNAP29 and ZNF74","Paternal","MLPA","(1 healthy brother, no DNA)"]
["Stage 1","3067_5","Male","MPX","CL","CL","European","22q11.21","22:19051464-19795780",744317,"Gain","20 genes, including MED15, SCARF2, SERPIND1, SLC7A4, SNAP29 and ZNF74","Paternal","qPCR","4 siblings: CNV present in 1 affected brother; absent in 1 affected male, 1 male with mild PDD, and 1 unaffected sister"]
["Stage 1","14230_3640","Male","SPX","Blood","Blood","European","22q11.21","22:19063495-19793730",730236,"Gain","20 genes, including MED15, SCARF2, SERPIND1, SLC7A4, SNAP29 and ZNF74","Maternal","qPCR","(not tested)"]
["Stage 1","5378_3","Male","MPX","Blood","Blood","European","22q11.21","22:19063495-19358946",295452,"Gain","KLHL22, MED15, SCARF2, ZNF74","Paternal","qPCR","present in 1 brother with ASD"]
["Stage 1","6057_3","Male","MPX","Blood","Blood","Other","22q11.21","22:19221842-19341132",119291,"Gain","MED15","Paternal","qPCR, MLPA","present in 1 brother with autism"]
["Stage 1","6340_3","Male","SPX","Blood","UNK (blood or CL)","European","22q11.21","22:20247190-20277644",30455,"Loss","UBE2L3","Both parents","qPCR","(3 sibs, no DNA)"]
["Stage 1","5453_4","Male","MPX","Blood","Blood","European","22q12.1","22:25718110-25730447",12338,"Gain","—","Maternal","qPCR","1 non-ASD brother, no CNV (another non-ASD brother, no CNV data)"]
["Stage 2","8630_201","Male","MPX","Blood","Blood","European","22q12.3","22:32346124-32413987",67864,"Loss (mosaic)","LARGE intronic","De novo","qPCR","(no siblings)"]
["Stage 2","2175_1","Male","SPX","Blood","Blood","European","22q13.2-q13.33","22:39729380-49582267",9852888,"None (mosaic UPD)","Mosaic 22q13 uniparental disomy (141 genes, including SHANK3)","De novo","validated by exclusion (normal MLPA)","(1 unaffected sibling, no DNA)","chromosomal abnormality, excluded from main analyses"]
["Stage 2","2072_1","Male","MPX","Blood","Blood","European","22q13.31-q13.33","22:45159185-49582267",4423083,"Loss","Phelan-McDermid syndrome (22q13 deletion, 47 genes including SHANK3)","De novo (germinal mosaicism)","qPCR","present in 1 sister with autism (2072_2)"]
["Stage 2","6130_4","Female","SPX","UNK (blood or CL)","UNK (blood or CL)","European","22q13.32-q13.33","22:47996161-49512530",1516370,"Loss","Phelan-McDermid syndrome (22q13 deletion, 37 genes including SHANK3)","De novo","qPCR, MLPA","(1 healthy sister, no DNA)"]
["Stage 2","14291_4120","Female","SPX","CL","CL","European","22q13.33","22:49470371-49480446",10076,"Loss","SHANK3","De novo","LR-PCR (sequencing coordinates: 49468716-49485255, size 16,540 bp)","(no siblings)"]
["Stage 2","16079_1571066001","Male","SPX","CL","CL","European","22q13.33","22:49470371-49567383",97013,"Loss","ACR, RABL2B, RPL23AP82, SHANK3","De novo","qPCR (mother has a DNA issue; not-paternal by qPCR; de novo DEL by plotting-visual inspection)","(2 unaffected siblings, not tested)"]
["Stage 2","4240_1","Male","SPX","Blood","Blood","European","Xp22.31","X:6459601-8095053",1635453,"Loss","HDHD1, MIR651, PNPLA4, STS, VCX, VCX3A","Maternal (X-linked in a male)","qPCR (Griswold et al. 2011, PMID: 21360829)","present in unaffected sister"]
["Stage 1","6239_3","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","Xp22.2","X:11324498-11418698",94201,"Gain","ARHGAP6 intronic","Maternal (X-linked in a male)","qPCR","(no siblings)"]
["Stage 1","6323_3","Male","SPX","Blood","UNK (blood or CL)","European","Xp22.2","X:14603137-14746120",142984,"Loss","GLRA2","Maternal (X-linked in a male)","qPCR","(no siblings)"]
["Stage 2","9900_203","Male","SPX","Blood","Blood","Other","Xp22.12","X:19396116-19509785",113670,"Gain","MAP3K15, SH3KBP1","Maternal (X-linked in a male)","qPCR","(not tested)"]
["Stage 2","17031_1","Male","SPX","Blood","Blood","European","Xp22.12","X:19450969-19845766",394798,"Loss","SH3KBP1, CXorf23","Maternal (X-linked in a male)","qPCR","(not tested)"]
["Stage 1","5521_3","Male","SPX","Blood","Blood","European","Xp22.12","X:19471138-19861338",390201,"Gain","CXorf23, SH3KBP1","Maternal (X-linked in a male)","qPCR","2 non-ASD sisters, no CNV in either"]
["Stage 2","16076_1571045001","Male","SPX","CL","CL","European","Xp22.11","X:22768481-23133948",365468,"Loss","DDX53 (upstream of PTCHD1)","De novo","qPCR","(1 unaffected sibling, not tested)"]
["Stage 1","13047_563","Male","MPX","Blood","Blood","European","Xp22.11","X:22829183-23214712",385530,"Loss","DDX53 (upstream of PTCHD1)","Maternal (X-linked in a male)","qPCR","(2 brothers with autism and 1 sister with pragmatic language disorder, no DNA)"]
["Stage 1","5111_3","Male","MPX","Blood","Blood","European","Xp22.11","X:22844170-22897714",53545,"Loss","— (upstream of PTCHD1)","Maternal (X-linked in a male)","qPCR, Illumina 1M-duo for sibs","1 brother with autism, no CNV;  CNV present in 1 non-ASD sister"]
["Stage 1","3253_4","Male","MPX","Buccal","Buccal","European","Xp22.11","X:22860224-22907454",47231,"Loss","— (upstream of PTCHD1)","Maternal (X-linked in a male)","qPCR","absent in 1 brother with autism and 1 unaffected younger sister"]
["Stage 1","5065_3","Male","MPX","Blood","Blood","European","Xp22.11","X:22860224-22923580",63357,"Loss","— (upstream of PTCHD1)","Maternal (X-linked in a male)","qPCR","1 brother with autism, no CNV"]
["Stage 1","5298_3","Male","MPX","Blood","Blood","European","Xp22.11","X:22892380-23013494",121115,"Loss","DDX53 (upstream of PTCHD1)","Maternal (X-linked in a male)","qPCR, Agilent 1M, Illumina 1M-duo for sibs","present in 1 non-ASD sister (5298_4)"]
["Stage 1","3424_3","Male","SPX","Blood","Blood","European","Xp22.11","X:23013250-23116188",102939,"Loss","— (upstream of PTCHD1)","Maternal (X-linked in a male)","qPCR","absent in 1 unaffected brother"]
["Stage 1","5240_4","Male","MPX","Blood","Blood","European","Xp22.11","X:23116188-23280628",164441,"Loss","PTCHD1","Maternal (X-linked in a male)","qPCR, Illumina 1M-duo for sibs","present in 1 DZ twin brother with autism (5240_5) and 1 non-ASD sister (5240_3)"]
["Stage 1","6032_4","Female","MPX","UNK (blood or CL)","UNK (blood or CL)","Other","Xp21.3","X:28732962-28751750",18789,"Loss","IL1RAPL1 intronic","Paternal","qPCR","absent in 1 maternal half-brother with autism, present in 1 healthy sister"]
["Stage 1","5126_4","Male","MPX","CL","CL","European","Xp21.2-p21.3","X:28931559-29478966",547408,"Gain","IL1RAPL1","Maternal (X-linked in a male)","qPCR, Agilent 1M","(1 brother with ASD, average IQ, epilepsy, abnormal brain MRI, no DNA) 4 unaffected sisters: CNV present in 2, absent in 1, no DNA for the other 2"]
["Stage 1","5036_4","Male","MPX","CL","CL","European","Xp21.2","X:29446046-29557942",111897,"Loss","IL1RAPL1 intronic","Maternal (X-linked in a male)","qPCR, Agilent 1M","present in 1 sister with Asperger and 1 non-ASD DZ triplet brother; absent in 1 non-ASD DZ triplet brother and 1 non-ASD sister"]
["Stage 2","6381_3","Male","SPX","Blood","Blood","European","Xp21.2","X:30521738-30789831",268094,"Gain","GK, TAB3","Maternal (X-linked in a male)","qPCR","(1 healthy brother, no DNA)"]
["Stage 2","8597_201","Male","SPX","Blood","Blood","European","Xp21.1-p21.2","X:31303978-32025062",721085,"Loss","DMD","Maternal (X-linked in a male)","qPCR","(not tested)"]
["Stage 1","5241_3","Male","MPX","Blood","Blood","European","Xp21.1","X:31793278-31822704",29427,"Loss","DMD","Maternal (X-linked in a male)","qPCR","1 brother with ASD, no CNV"]
["Stage 1","3019_3","Male","MPX","Buccal","Buccal","European","Xp21.1","X:32100618-32315937",215320,"Gain","DMD","Maternal (X-linked in a male)","qPCR, LR-PCR (sequencing coordinates: chrX:3209213-32321945, size: 224,733 bp), FISH (Pagnamenta et al. 2011, PMID: 21484199 )","CNV present in affected brother, absent in healthy sister"]
["Stage 1","5126_4","Male","MPX","CL","CL","European","Xp21.1","X:32948977-33330592",381616,"Gain","DMD","Maternal (X-linked in a male)","qPCR, Agilent 1M","(1 brother with ASD, average IQ, epilepsy, abnormal brain MRI, no DNA) 4 unaffected sisters: CNV present in 2, absent in 1, no DNA for the other 2"]
["Stage 2","20032_1226001","Male","MPX","Blood","Blood","European","Xp21.1","X:34073457-34123587",50131,"Loss","—","Maternal (X-linked in a male)","qPCR","(not tested)"]
["Stage 2","20141_1396001","Male","SPX","Blood","Blood","European","Xp11.4","X:38375788-38515190",139403,"Gain","TSPAN7","Maternal (X-linked in a male)","qPCR","CNV also present in unaffected sister"]
["Stage 2","9861_202","Male","SPX","Blood","Blood","Other","Xp11.4","X:41248675-41259467",10793,"Gain","CASK","Maternal (X-linked in a male)","qPCR","(not tested)"]
["Stage 1","5419_3","Male","SPX","CL","CL","European","Xp11.4","X:41441499-41478503",37005,"Gain","CASK intronic, GPR82","Maternal (X-linked in a male)","qPCR","(no siblings)"]
["Stage 1","5007_3","Male","MPX","Blood","Blood","European","Xp11.3","X:46255974-46292959",36986,"Gain","LOC401588, ZNF674","Maternal (X-linked in a male)","qPCR, Illumina 1M-duo for sibs","1 brother with autism and 1 non-ASD brother, no CNV in either"]
["Stage 2","17018_1","Male","SPX","Blood","Blood","Other","Xp11.22","X:53568262-53640902",72641,"Gain","HUWE1, MIR98, MIRLET7F2","Maternal (X-linked in a male)","qPCR","(no siblings)"]
["Stage 2","14314_4310","Male","SPX","Blood","Blood","European","Xq13.1","X:70865247-71509736",644490,"Gain","13 genes, including CITED1, ERCC6L, HDAC8, NHSL2, RPS26P11 and RPS4X","Maternal (X-linked in a male)","qPCR","(3 healthy sibs —2 boys and 1 girl— not tested) "]
["Stage 2","8617_201","Male","UNK","Blood","Blood","European","Xq13.2","X:72212796-72267781",54986,"Gain","NAP1L6, PABPC1L2A","Maternal (X-linked in a male)","qPCR","(not tested)"]
["Stage 2","18113_302","Female","MPX","CL","CL","European","Xq13.3","X:74319353-74380018",60666,"Gain","—","Paternal","qPCR","1 affected sib with deletion of the same region, 1 affected sib with duplication of the same region"]
["Stage 1","5209_3","Male","MPX","CL","CL","European","Xq21.33","X:95936387-95949943",13557,"Gain","DIAPH2 intronic","Maternal (X-linked in a male)","qPCR","present in 1 brother with autism (5209_4); absent in 1 non-ASD sister"]
["Stage 1","5468_3","Male","SPX","Blood","Blood","European","Xq22.3","X:107765808-107890152",124345,"Gain","COL4A5, IRS4","Maternal (X-linked in a male)","qPCR, Illumina 1M-duo for sib","present in 1 non-ASD sister"]
["Stage 1","6239_3","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","Xq27.1","X:138549326-138716662",167337,"Gain","ATP11C, MCF2","Maternal (X-linked in a male)","qPCR","(no siblings)"]
["Stage 1","1348_301","Male","MPX","CL","CL","Other","Xq28","X:147163528-147758700",595173,"Gain","AFF2","Maternal (X-linked in a male)","qPCR","no CNV in sister with autism"]
["Stage 1","5286_3","Male","SPX","Blood","Blood","European","Xq28","X:148493841-148543935",50095,"Loss","TMEM185A","Maternal (X-linked in a male)","qPCR, Illumina 1M-duo for sibs","present in 1 non-ASD brother and absent in 1 non-ASD maternal half-sister"]
["Stage 2","20128_4016001","Male","SPX","Blood","Blood","European","Xq28","X:148502746-148542439",39694,"Gain","TMEM185A","Maternal (X-linked in a male)","qPCR","(no siblings)"]
["Stage 2","20013_1075001","Male","SPX","CL","CL","European","Xq28","X:153239048-153521797",282750,"Gain","Xq28 duplication (20 genes, including GDI1)","De novo","qPCR, LR-PCR (sequencing coordinates: chrX:153,222,048-153,514,311, size 292,264 bp)","(unaffected younger brother and sister, not tested)"]
["Stage 1","14216_3470","Male","SPX","Blood","Blood","European","Xq28","X:153263157-153474401",211245,"Gain","Xq28 duplication (18 genes, including GDI1)","Maternal (X-linked in a male)","qPCR","1 brother with developmental delay tested also carries CNV","Astrid replied that after repeating it gave maternal"]
["Stage 1","6175_6 ","Male","SPX","UNK (blood or CL)","UNK (blood or CL)","European","Xq28","X:154442377-154515181",72805,"Gain","TMLHE","Maternal (X-linked in a male)","qPCR","(4 healthy sibs, no DNA)"]
["Stage 1","14186_3050","Male","SPX","Blood","Blood","European","Xq28","X:154569169-154582606",13438,"Loss","—","Maternal (X-linked in a male)","qPCR","(1 healthy brother, no DNA)"]
["Stage 1","14144_2420","Male","SPX","Blood","Blood","European","Xq28","X:154569169-154582606",13438,"Loss","—","Maternal (X-linked in a male)","qPCR","(1 healthy sister, no DNA)"]
["Stage 1","14198_3220","Male","MPX","Blood","Blood","European","Xq28","X:154569169-154582606",13438,"Loss","—","Maternal (X-linked in a male)","qPCR","(no siblings)"]
["Stage 1","5257_3","Male","SPX","Blood","Blood","European","Yp11.32-q12","Y:1-57772954",57772954,"Gain","XYY syndrome","De novo","karyotype","(not tested)","chromosome abnormality"]
["Stage 1","5515_3","Male","SPX","Blood","Blood","European","Yp11.32-q12","Y:1-57772954",57772954,"Gain","XYY syndrome","De novo","karyotype","(not tested)","chromosome abnormality"]