T1  Age 18 28   3-year-old

T2  Sex 29 33   girl

T3  Diagnostic_procedure 65 84  VACTERL association

E1  Diagnostic_procedure:T3 

T8  Subject 554 564 her father

T9  Disease_disorder 626 648    Ehlers–Danlos syndrome

E6  Disease_disorder:T9 

T10 History 626 648 Ehlers–Danlos syndrome

T12 Detailed_description 609 625    hypermobile type

R2  MODIFY Arg1:T12 Arg2:E6 

T13 Disease_disorder 485 503    limb malformations

E8  Disease_disorder:T13 

A1  POLARITY E8 NEG

T14 Disease_disorder 512 539    other major organ anomalies

E9  Disease_disorder:T14 

T15 Disease_disorder 474 481;490 503    cardiac malformations

E10 Disease_disorder:T15 

A2  POLARITY E10 NEG

*   OVERLAP E10 E8 E1

T16 Disease_disorder 734 747    Ehlers–Danlos

E11 Disease_disorder:T16 

T17 Detailed_description 717 733    hypermobile type

R5  MODIFY Arg1:T17 Arg2:E11    

T18 Diagnostic_procedure 2831 2853  DNA Polymerase Gamma 1

E12 Diagnostic_procedure:T18 

T19 Diagnostic_procedure 2831 2851;2858 2859    DNA Polymerase Gamma 2

E13 Diagnostic_procedure:T19 

T20 Diagnostic_procedure 2861 2866  POLG1

E14 Diagnostic_procedure:T20 

T21 Diagnostic_procedure 2871 2876  POLG2

E15 Diagnostic_procedure:T21 

R6  IDENTICAL Arg1:E15 Arg2:E13 

R7  IDENTICAL Arg1:E14 Arg2:E12 

T22 Diagnostic_procedure 2882 2905  Thymidine Phosphorylase

E16 Diagnostic_procedure:T22 

T23 Diagnostic_procedure 2817 2827  sequencing

E17 Diagnostic_procedure:T23 

R8  SUB_PROCEDURE Arg1:E13 Arg2:E17 

R9  SUB_PROCEDURE Arg1:E13 Arg2:E17 

R10 SUB_PROCEDURE Arg1:E16 Arg2:E17 

A3  POLARITY E12 NEG

A4  POLARITY E13 NEG

A5  POLARITY E16 NEG

T24 Diagnostic_procedure 2794 2811  genome sequencing

E18 Diagnostic_procedure:T24 

T25 Biological_structure 2780 2793  mitochondrial

T26 Detailed_description 2774 2779  Whole

R11 MODIFY Arg1:T26 Arg2:T25    

R12 MODIFY Arg1:T25 Arg2:E18    

*   OVERLAP E18 E17 E21

T27 Diagnostic_procedure 2637 2662  Citrate synthase activity

E19 Diagnostic_procedure:T27 

T28 Lab_value 2701 2707 normal

T29 Diagnostic_procedure 2725 2739  sample quality

E20 Diagnostic_procedure:T29 

T30 Diagnostic_procedure 2751 2772  mitochondrial content

E21 Diagnostic_procedure:T30 

T31 Lab_value 2744 2750 normal

T32 Lab_value 2720 2724 good

R13 MODIFY Arg1:T32 Arg2:E20    

R14 MODIFY Arg1:T31 Arg2:E21    

T33 Coreference 2678 2695   both ETC analyses

E22 Coreference:T33 

T34 Diagnostic_procedure 2637 2653;2667 2674    Citrate synthase content

E23 Diagnostic_procedure:T34 

T35 Diagnostic_procedure 2538 2550  ETC analysis

E24 Diagnostic_procedure:T35 

T36 Detailed_description 2531 2537  Repeat

T37 Biological_structure 2563 2575  mitochondria

T38 Detailed_description 2554 2562  isolated

R15 MODIFY Arg1:T38 Arg2:T37    

R16 MODIFY Arg1:T36 Arg2:E24    

R17 MODIFY Arg1:T37 Arg2:E24    

T39 Disease_disorder 2614 2635  complex IV deficiency

E25 Disease_disorder:T39 

T40 Severity 2588 2596  profound

T41 Detailed_description 2601 2613  reproducible

R18 MODIFY Arg1:T41 Arg2:E25    

R19 MODIFY Arg1:T40 Arg2:E25    

R20 MODIFY Arg1:E25 Arg2:E24    

T42 Diagnostic_procedure 2296 2320;2327 2335    electron transport chain activity

E26 Diagnostic_procedure:T42 

T43 Diagnostic_procedure 2321 2335  (ETC) activity

E27 Diagnostic_procedure:T43 

R21 IDENTICAL Arg1:E27 Arg2:E26 

T44 Diagnostic_procedure 2392 2402  complex IV

E28 Diagnostic_procedure:T44 

T45 Diagnostic_procedure 2362 2373  complexes I

E29 Diagnostic_procedure:T45 

T46 Diagnostic_procedure 2362 2371;2375 2377    complexes II

E30 Diagnostic_procedure:T46 

T47 Diagnostic_procedure 2362 2371;2383 2386    complexes III

E31 Diagnostic_procedure:T47 

T48 Lab_value 2343 2349 normal

R22 SUB_PROCEDURE Arg1:E29 Arg2:E26 

R23 SUB_PROCEDURE Arg1:E30 Arg2:E26 

R24 SUB_PROCEDURE Arg1:E31 Arg2:E26 

R25 SUB_PROCEDURE Arg1:E28 Arg2:E26 

R26 MODIFY Arg1:T48 Arg2:E31    

R27 MODIFY Arg1:T48 Arg2:E30    

R28 MODIFY Arg1:T48 Arg2:E29    

T49 Diagnostic_procedure 2407 2427  cytochrome c oxidase

E32 Diagnostic_procedure:T49 

R29 IDENTICAL Arg1:E32 Arg2:E28 

T50 Lab_value 2442 2464 45.4 lmol/min/g weight

R30 MODIFY Arg1:T50 Arg2:E32    

T51 Diagnostic_procedure 2123 2129  biopsy

E33 Diagnostic_procedure:T51 

T52 Biological_structure 2116 2122  Muscle

R31 MODIFY Arg1:T52 Arg2:E33    

T53 Diagnostic_procedure 2156 2178  fiber size variability

E34 Diagnostic_procedure:T53 

T54 Lab_value 2144 2152 increase

T55 Severity 2139 2143  mild

R32 MODIFY Arg1:T55 Arg2:T54    

R33 MODIFY Arg1:T54 Arg2:E34    

R34 SUB_PROCEDURE Arg1:E34 Arg2:E33 

T56 Diagnostic_procedure 2254 2273  electron microscopy

E35 Diagnostic_procedure:T56 

T58 Age 1820 1836   13 months of age

T59 Sign_symptom 1854 1869  muscle weakness

E37 Sign_symptom:T59 

T60 Detailed_description 1842 1853  progressive

R36 MODIFY Arg1:T60 Arg2:E37    

T61 Disease_disorder 1871 1894  autonomic dysregulation

E38 Disease_disorder:T61 

T62 Disease_disorder 1896 1917  hypoglycemic episodes

E39 Disease_disorder:T62 

T63 Disease_disorder 1919 1950  exocrine pancreatic dysfunction

E40 Disease_disorder:T63 

T64 Diagnostic_procedure 1967 1992  gastrointestinal function

E41 Diagnostic_procedure:T64 

T65 Detailed_description 1956 1963  decline

R37 MODIFY Arg1:T65 Arg2:E41    

T66 Disease_disorder 2070 2082  hyperalgesia

E42 Disease_disorder:T66 

T67 Biological_structure 2061 2069  visceral

R38 MODIFY Arg1:T67 Arg2:E42    

T68 Disease_disorder 2084 2095  dysmotility

E43 Disease_disorder:T68 

T69 Disease_disorder 2101 2114  malabsorption

E44 Disease_disorder:T69 

T70 Disease_disorder 2033 2053  nutrition dependency

E45 Disease_disorder:T70 

T71 Severity 2016 2021  total

T72 Detailed_description 2022 2032  parenteral

R39 MODIFY Arg1:T72 Arg2:E45    

R40 MODIFY Arg1:T71 Arg2:T72    

T73 Diagnostic_procedure 1165 1169  FISH

E46 Diagnostic_procedure:T73 

T74 Diagnostic_procedure 907 913    biopsy

E47 Diagnostic_procedure:T74 

T75 Biological_structure 902 906    Skin

R41 MODIFY Arg1:T75 Arg2:E47    

T76 Disease_disorder 1021 1043  Ehlers–Danlos syndrome

E48 Disease_disorder:T76 

T77 Diagnostic_procedure 980 989    mutations

E49 Diagnostic_procedure:T77 

A7  POLARITY E49 NEG

T78 Detailed_description 1006 1017  other forms

R42 MODIFY Arg1:T78 Arg2:E48    

T79 Biological_structure 948 964    peripheral blood

T80 Diagnostic_procedure 937 944    testing

E50 Diagnostic_procedure:T80 

R43 MODIFY Arg1:T79 Arg2:E50    

A8  POLARITY E47 NEG

T81 Texture 837 841 soft

T82 Texture 843 850 fragile

T83 Lab_value 832 836   very

R44 MODIFY Arg1:T83 Arg2:T81    

R45 MODIFY Arg1:T83 Arg2:T82    

T84 Biological_structure 851 855    skin

R46 MODIFY Arg1:T81 Arg2:T84    

R47 MODIFY Arg1:T82 Arg2:T84    

T85 Detailed_description 861 877    unusual scarring

R48 MODIFY Arg1:T85 Arg2:T84    

T86 Detailed_description 888 900    skin healing

T87 Lab_value 883 887   poor

R49 MODIFY Arg1:T87 Arg2:T86    

R50 MODIFY Arg1:T86 Arg2:T84    

T88 Diagnostic_procedure 1045 1064  Microarray analysis

E51 Diagnostic_procedure:T88 

T89 Biological_structure 1117 1123  4q35.1

#1  AnnotatorNotes T89  Chromosome location

T90 Diagnostic_procedure 1105 1113  deletion

E52 Diagnostic_procedure:T90 

T91 Detailed_description 1084 1104  maternally-inherited

R51 MODIFY Arg1:T91 Arg2:E52    

R52 MODIFY Arg1:T89 Arg2:E52    

R53 SUB_PROCEDURE Arg1:E52 Arg2:E51 

T92 Diagnostic_procedure 1138 1147  one clone

E53 Diagnostic_procedure:T92 

T93 Disease_disorder 775 788    hypermobility

E54 Disease_disorder:T93 

T94 Diagnostic_procedure 801 829    Beighton hypermobility scale

E55 Diagnostic_procedure:T94 

T95 Lab_value 790 793   9/9

R54 MODIFY Arg1:T95 Arg2:E55    

R55 MODIFY Arg1:E55 Arg2:E54    

T96 Disease_disorder 1785 1810  mitochondrial dysfunction

E56 Disease_disorder:T96 

T97 Diagnostic_procedure 1214 1252  180K custom oligonucleotide microarray

E57 Diagnostic_procedure:T97 

T98 Nonbiological_location 1254 1310    Baylor College of Medicine Medical Genetics Laboratories

T99 Lab_value 1353 1376 maximum size of 1.37 Mb

T100    Lab_value 218 223   three

T101    Subject 1707 1717   her mother

T104    Detailed_description 1719 1755  from whom the deletion was inherited

R57 MODIFY Arg1:T104 Arg2:T101  

T105    Diagnostic_procedure 1599 1605  CYP4V2

E59 Diagnostic_procedure:T105 

T106    Diagnostic_procedure 1607 1612  KLKB2

E60 Diagnostic_procedure:T106 

T107    Diagnostic_procedure 1614 1617  F11

E61 Diagnostic_procedure:T107 

T108    Diagnostic_procedure 1619 1626  MTRNR1A

E62 Diagnostic_procedure:T108 

T109    Diagnostic_procedure 1632 1636  FAT1

E63 Diagnostic_procedure:T109 

*   OVERLAP E62 E61 E60 E59

T4  Biological_structure 120 136    lumbar vertebrae

T5  Biological_structure 93 104 C1 vertebra

T110    Detailed_description 86 92  absent

T111    Detailed_description 106 119    supernumerary

R58 MODIFY Arg1:T110 Arg2:T5    

R59 MODIFY Arg1:T111 Arg2:T4    

T6  Biological_structure 150 156    sacrum

T112    Biological_structure 157 163    coccyx

T113    Detailed_description 138 149    hypoplastic

R60 MODIFY Arg1:T113 Arg2:T6    

R61 MODIFY Arg1:T113 Arg2:T112  

T114    Biological_structure 171 186    filum terminale

T115    Biological_structure 201 212    spinal cord

T116    Biological_structure 230 234    ribs

T117    Detailed_description 224 229    fused

R62 MODIFY Arg1:T117 Arg2:T116  

R63 MODIFY Arg1:T100 Arg2:T116  

T118    Detailed_description 192 200    tethered

T119    Detailed_description 165 170    fatty

R64 MODIFY Arg1:T119 Arg2:T114  

R65 MODIFY Arg1:T118 Arg2:T115  

T7  Disease_disorder 239 261    anorectal malformation

E2  Disease_disorder:T7 

T11 Biological_structure 274 280    cloaca

T120    Biological_structure 334 340    vagina

T121    Biological_structure 304 320    urogenital sinus

T122    Detailed_description 297 303    common

R1  MODIFY Arg1:T122 Arg2:T121  

T123    Detailed_description 327 333    duplex

R4  MODIFY Arg1:T123 Arg2:T120  

T124    Detailed_description 346 360    midline septum

R66 MODIFY Arg1:T124 Arg2:T120  

T125    Disease_disorder 369 379    TE fistula

E3  Disease_disorder:T125 

T126    Detailed_description 362 368    type C

R67 MODIFY Arg1:T126 Arg2:E3    

T127    Disease_disorder 393 401    agenesis

E4  Disease_disorder:T127 

T128    Biological_structure 381 392    right renal

R68 MODIFY Arg1:T128 Arg2:E4    

T129    Disease_disorder 421 435    hydronephrosis

E5  Disease_disorder:T129 

T130    Disease_disorder 440 461    vesicoureteral reflux

E7  Disease_disorder:T130 

T131    Severity 407 415    moderate

T132    Detailed_description 416 420    left

R69 MODIFY Arg1:T132 Arg2:E5    

R70 MODIFY Arg1:T131 Arg2:E5    

R71 MODIFY Arg1:T5 Arg2:E1  

R72 MODIFY Arg1:T4 Arg2:E1  

R73 MODIFY Arg1:T6 Arg2:E1  

R74 MODIFY Arg1:T112 Arg2:E1    

R75 MODIFY Arg1:T114 Arg2:E1    

R76 MODIFY Arg1:T115 Arg2:E1    

R77 MODIFY Arg1:T116 Arg2:E1    

R78 MODIFY Arg1:E2 Arg2:E1  

R79 MODIFY Arg1:T11 Arg2:E2 

R80 MODIFY Arg1:T121 Arg2:T11   

R81 MODIFY Arg1:T120 Arg2:T11   

R82 MODIFY Arg1:E3 Arg2:E1  

R83 MODIFY Arg1:E4 Arg2:E1  

R84 BEFORE Arg1:E5 Arg2:E1  

R85 MODIFY Arg1:E7 Arg2:E1  

A9  POLARITY E9 NEG

R86 BEFORE Arg1:E10 Arg2:E9 

R87 MODIFY Arg1:E54 Arg2:E11    

R88 MODIFY Arg1:T84 Arg2:E11    

R89 MODIFY Arg1:T86 Arg2:E11    

*   OVERLAP E11 E47 E50 E9

R90 SUB_PROCEDURE Arg1:E49 Arg2:E50 

R91 MODIFY Arg1:E48 Arg2:E49    

*   OVERLAP E48 E51

R92 SUB_PROCEDURE Arg1:E53 Arg2:E52 

R93 SUB_PROCEDURE Arg1:E46 Arg2:E52 

T133    Diagnostic_procedure 1170 1183  (RP11-173M11)

E64 Diagnostic_procedure:T133 

R94 IDENTICAL Arg1:E64 Arg2:E46 

R95 BEFORE Arg1:E64 Arg2:E57    

R96 MODIFY Arg1:T98 Arg2:E57    

T134    Diagnostic_procedure 1383 1392  karyotype

E65 Diagnostic_procedure:T134 

T135    Detailed_description 1404 1459  46,XX,arr cgh 4q35.1q35.2 (187,321-768-188,694-589) 3 1

R97 MODIFY Arg1:T135 Arg2:E65   

R98 SUB_PROCEDURE Arg1:E65 Arg2:E57 

T136    Diagnostic_procedure 1324 1347  deleted region deletion

E66 Diagnostic_procedure:T136 

R99 MODIFY Arg1:T99 Arg2:E66    

R100    SUB_PROCEDURE Arg1:E66 Arg2:E57 

*   OVERLAP E53 E46

T137    Diagnostic_procedure 1461 1466  Genes

E67 Diagnostic_procedure:T137 

T138    Detailed_description 1474 1488  deleted region

R101    MODIFY Arg1:T138 Arg2:E67   

R102    SUB_PROCEDURE Arg1:E59 Arg2:E67 

R103    SUB_PROCEDURE Arg1:E60 Arg2:E67 

R104    SUB_PROCEDURE Arg1:E61 Arg2:E67 

R105    SUB_PROCEDURE Arg1:E62 Arg2:E67 

R106    SUB_PROCEDURE Arg1:E63 Arg2:E67 

T103    Disease_disorder 1760 1770  unaffected

E68 Disease_disorder:T103 

A10 POLARITY E68 NEG

T139    Family_history 1760 1770    unaffected

R56 MODIFY Arg1:E68 Arg2:T101   

R107    AFTER Arg1:E67 Arg2:E56 

R108    MODIFY Arg1:E37 Arg2:E56    

*   OVERLAP E37 E38 E39 E40 E41

R109    BEFORE Arg1:E41 Arg2:E45    

R110    CAUSE Arg1:E42 Arg2:E45 

R111    CAUSE Arg1:E43 Arg2:E45 

R112    CAUSE Arg1:E44 Arg2:E45 

*   OVERLAP E42 E43 E44 E33

R113    MODIFY Arg1:E41 Arg2:E56    

R114    MODIFY Arg1:E40 Arg2:E56    

R115    MODIFY Arg1:E39 Arg2:E56    

R116    MODIFY Arg1:E38 Arg2:E56    

R117    MODIFY Arg1:E37 Arg2:E56    

T57 Diagnostic_procedure 2186 2200  other findings

E36 Diagnostic_procedure:T57 

A6  POLARITY E36 NEG

T102    Detailed_description 2201 2238  consistent with mitochondrial disease

R35 MODIFY Arg1:T102 Arg2:E36   

R118    SUB_PROCEDURE Arg1:E35 Arg2:E36 

R119    SUB_PROCEDURE Arg1:E36 Arg2:E33 

*   OVERLAP E34 E36

*   OVERLAP E35 E26

T140    Detailed_description 2466 2494  well below the control range

R120    MODIFY Arg1:T140 Arg2:T50   

*   OVERLAP E32 E24

*   OVERLAP E25 E19

R121    IDENTICAL Arg1:E22 Arg2:E27 

R122    IDENTICAL Arg1:E22 Arg2:E24 

R123    SUB_PROCEDURE Arg1:E23 Arg2:E22 

R124    SUB_PROCEDURE Arg1:E19 Arg2:E22 

R125    MODIFY Arg1:T28 Arg2:E19    

R126    MODIFY Arg1:T28 Arg2:E23    

R127    SUB_PROCEDURE Arg1:E20 Arg2:E22 

R128    SUB_PROCEDURE Arg1:E21 Arg2:E22 

T141    Family_history 626 648  Ehlers–Danlos syndrome

R3  MODIFY Arg1:E6 Arg2:T8  

T142    Other_entity 546 549    she

#2  AnnotatorNotes T142 Patient herself

R129    MODIFY Arg1:E6 Arg2:T142