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1 Supporting Information Yin et al /pnas Fig. S1. Characteristic Z scores of a section of DNA encompassing a deletion in sample 14,945 at (A) varying concentrations of abnormal DNA at 5 million and (B) varying sequencing depths at 15% concentration of abnormal DNA. (C) The acgh plot of sample 14,945 is shown for comparison. 1of5
2 Fig. S2. Distribution of fetal DNA concentrations estimated of maternal plasma in a cohort of 1,476 pregnant women at various gestational ages. Table S1. s of newborns with DNA deletions and duplications Chr Start End Size (Mb) Syndrome annotation 14,437 Del Chr p13.11 Microdeletion (neurocognitive disorder susceptibility locus) 14,394 Del Chr Thrombocytopenia-absent radius 14,416 Dup Chr Phelan Mcdermid Syndrome/22q13 14,452 Del Chr Cri du Chat Syndrome (5p deletion) 14,944 Del Chr Uncertain 14,095 Del Chr Uncertain 14,368 Del Chrx Xp21 14,209 Del Chr Potocki Lupski Syndrome (17p11.2 duplication ) 14,181 Del Chr Uncertain 14,777 Del Chr DiGeorge Syndrome/22q ,095 Del Chr Rubinstein Taybi 14,540 Del Chr Prader Willi/Angelman 14,883 Del Chr Uncertain 14,157 Del Chr Uncertain 14,119 Del Chr q Deletion 14,159 Del Chr Hypoparathyroidism, sensorineural deafness, and renal disease (HDRS) 14,115 Del Chr Wolf Hirschhorn 14,873 Dup Chr q31.1 Duplication 14,452 Dup Chr q25 Deletion 14,945 Del Chr Uncertain 14,798 Del Chr Uncertain 14,181 Dup Chr p Deletion Chr, chromosome; Del, deletion; Dup, duplication. 2of5
3 Table S2. Comparison of NIPT and acgh in clinical samples A0587 Del Chr16: p11.2 Microduplication No No No No A0133 Dup Chr19: No No No No A0553 Del Chr19: No No No No A0519 Del Chr3: p Syndrome 9.57 No No No No A0957 Del Chr7: q Deletion No No No No A0281 Del Chr17: p13.1 Deletion 9.76 No No No No A1005 Dup Chr22: q11.2 Deletion Chr22: No No Yes Yes A1102 Dup Chr2: Chr2: Yes Yes Yes Yes A1444 Del Chr17: q25 Duplication Chr17: No No Yes Yes A0187 Del Chrx: Steroid sulphatase NA Chrx: Yes Yes Yes Yes A0197 Dup Chrx: Steroid sulphatase 9.61 Chrx: Yes Yes Yes Yes A0403 Del Chrx: Steroid sulphatase Chrx: Yes Yes Yes Yes A1042 Dup Chr18: p11.32-p11.31 Duplication Chr18: No No Yes Yes A1138 Dup Chr18: q Deletion Chr18: No No Yes Yes A0495 Dup Chr16: p13.11 Microdeletion Chr16: Yes Yes Yes Yes A1285 Del Chr17: Chr17: No No Yes Yes A0844 Dup Chr8:1.44e e q22.1-qter Duplication No No No No A1034 Del Chr4: q11-q22 Deletion Chr4: No No Yes Yes A0248 Del Chr4: Chr4: Yes Yes Yes Yes A0129 Dup Chr4:1.57e e q32.1-q32.2 Triplication A0769 Del Chr22: DiGeorge Syndrome/22q11.2 A0286 Dup Chr22: DiGeorge Syndrome/22q Chr4: Yes Yes Yes Yes NA No No No No Chr22: Yes Yes Yes Yes A0686 Del Chr6: pter-p24 Deletion NA Chr6: No No Yes Yes A0901 Del Chr13: Chr13: No No Yes Yes A0786 Dup Chr21: Chr21: No No Yes Yes A0301 Del Chr2:1.72e e Chr2: Yes Yes Yes Yes A0310 Del Chr22: DiGeorge Syndrome/22q Chr22: Yes Yes Yes Yes A0580 Dup Chr11:1.31e e Jacobsen Syndrome 8.68 Chr11: No No Yes Yes A1052 Dup Chry: Chry: Yes Yes Yes Yes A0001 Del Chr1: p36 Micro Chr1: Yes Yes Yes Yes A0109 Dup Chr17: Smith Magenis Syndrome Chr17: Yes Yes Yes Yes A0142 Del Chr22: DiGeorge Syndrome/22q Chr22: No Yes Yes Yes A1012 Del Chr1: p Deletion Chr1: Yes Yes Yes Yes 3of5
4 Table S2. Cont. A0844 Del Chr21: Chr21: No No Yes Yes A0901 Dup Chry: AZFb NA Chry: Yes Yes Yes Yes A0433 Dup Chr15: q11.2 Deletion Chr15: Yes Yes Yes Yes A0899 Del Chr6:1.65e e Microdeletion 6q27 anosmia 8.93 Chr6: No Yes Yes Yes A0947 Dup Chr15: Prader Willi Syndrome (type 2) Chr15: Yes Yes Yes Yes A0133 Del Chr14:1.01e e No No No No A0001 Dup Chr19: Chr19: Yes Yes Yes Yes A0202 Dup Chr22: DiGeorge Syndrome/22q Chr22: Yes Yes Yes Yes A0894 Dup Chr3:1.90e e q29 Micro Chr3: Yes Yes Yes Yes A0786 Del Chr4: Wol Hirschhorn Syndrome Chr4: Yes Yes Yes Yes A0107 Dup Chry: AZFa Chry: Yes Yes Yes Yes A0107 Del Chry: Sex-determining region Y/SRY Chry: Yes Yes Yes Yes A0011 Del Chr4: Wolf Hirschhorn Syndrome Chr4: Yes Yes Yes Yes A0256 Dup Chr12: p13.33 Microdeletion Chr12: Yes Yes Yes Yes A0578 Del Chr18: p Deletion Chr18: Yes Yes Yes Yes A0676 Del Chr4:1.78e e ASD; small omphalocele, 8.54 Chr4: Yes Yes Yes Yes anteriorly placed anus, cleft palate A0248 Del Chr4: q21 Deletion Chr4: Yes Yes Yes Yes A0577 Dup Chr18: p Deletion Chr18: Yes Yes Yes Yes A0856 Del Chr13:1.01e e Chr13: Yes Yes Yes Yes A0322 Dup Chr17: p13.1 Deletion NA Chr17: Yes Yes Yes Yes A0359 Del Chr18: p Deletion Chr18: Yes Yes Yes Yes A0652 Dup Chr13: e Chr13: Yes Yes Yes Yes A1092 Dup Chr18: p11.32-p11.31 Duplication Chr18: Yes Yes Yes Yes A0580 Del Chr15: q25 Deletion 8.68 Chr15: Yes Yes Yes Yes A0310 Dup Chr11:1.17e e Jacobsen Chr11: Yes Yes Yes Yes A0953 Del Chr4: p Deletion 9.45 Chr4: Yes Yes Yes Yes A0676 Dup Chr3: p Syndrome 8.54 Chr3: Yes Yes Yes Yes A0856 Dup Chr5: Cri du Chat Syndrome Chr5: Yes Yes Yes Yes (5p deletion) A0686 Dup Chr10:1.14e e q26 Deletion NA Chr10: Yes Yes Yes Yes A0224 Dup Chr7:1.37e e Chr7: Yes Yes Yes Yes A1073 Dup Chr2: q31.1 Duplication 9.78 Chr2: Yes Yes Yes Yes A0202 Dup Chr7:1.36e e Chr7: Yes Yes Yes Yes A0359 Del Chr18: q Deletion Chr18: Yes Yes Yes Yes A0302 Dup Chr13: e Chr13: Yes Yes Yes Yes A0644 Del Chr13: q14 Deletion Chr13: Yes Yes Yes Yes A0224 Dup Chr13: e Chr13: Yes Yes Yes Yes A0894 Del Chr13: e Chr13: Yes Yes Yes Yes A0256 Dup Chr14: q11-q22 Deletion Chr14: Yes Yes Yes Yes 4of5
5 Table S2. Cont. A0519 Dup Chr18: q Deletion 9.57 Chr18: Yes Yes Yes Yes A0093 Dup Chr5: Cri du Chat Syndrome NA Chr5: Yes Yes Yes Yes (5p deletion) A0403 Dup Chr21: Early-onset Alzheimer Chr21: Yes Yes Yes Yes disease with cerebral amyloid angiopathy A0322 Del Chrx: Xp11.22-p11.23 microduplication NA Chrx: Yes Yes Yes Yes A0899 Dup Chr2:1.90e e q33.1 Deletion 8.93 Chr2: Yes Yes Yes Yes A0971 Del Chrx: Xq26-28 deletion Chrx: Yes Yes Yes Yes A0632 Dup Chr9: p Deletion Chr9: Yes Yes Yes Yes ASD, atrial septal defect; AZFa, azoospermia factor region a; AZFb, azoospermia factor region b; Chr, chromosome; Del, deletion; Dup, duplication; FC, fetal DNA concentration; NA, not applicable. *Syndrome is associated with either deletion or duplication in the region but may not match the observed DNA abnormality. 5of5
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