Method for screening a subject for cancer

Abstract

The present invention relates to the diagnostic of cancerous subject. Indeed, the inventors observed by using a Q-PCR based methods and sequencing methods that quantification of specific single stranded DNA fragments obtained from cell free nucleic acids (cfDNA) may discriminate cfDNA from healthy and cancer derived subjects. Single stranded DNA fragments obtained from CfDNA or specific range of single stranded DNA fragments are rather lower or higher when derived from healthy subject than from cancer subject. More, specific ratios for different size or range of single stranded DNA fragments varies between cancer subjects and healthy individuals. These values are sufficiently and significantly different to be used as values to determine whether a human subject may have cancer or not as a screening test. Thus, the invention relates to a method for screening a subject for a cancer comprising the steps of extracting and denaturing cfDNA, determining the single strand fragment level upon their size distribution, and calculate these former values to screen an individual for cancer.

1 . A method of screening and treating a subject for a cancer, comprising the steps of:
 i. extracting cell free DNA (cfDNA) from a sample obtained from the subject;   ii. denaturating the cfDNA to obtain single stranded DNA fragments;   iii. measuring a level of at least one single stranded DNA fragment having a length between 20 to 400 nucleotides;   iv. comparing the level of the at least one single stranded DNA fragment with a predetermined reference value; and   v. administering one or more cancer treatments to a subject identified as having a higher level than a predetermined reference value of at least one single stranded DNA fragment having a length less than 160 nucleotides and/or a lower level than a predetermined reference value of at least one single stranded DNA fragment having a length equal to or greater than 160 nucleotides, wherein the one or more cancer treatments are selected from the group consisting of radiotherapy, chemotherapy and immunotherapy.   
     
     
         2 . The method according to the  claim 1 , further comprising the steps of:
 i. measuring a level of a first single stranded DNA fragment having a length between 20 to 400 nucleotides;   ii. measuring a level of a second single stranded DNA fragment having a length between 20 to 400 nucleotides;   iii. calculating a ratio of the level of the first single stranded DNA fragment to the level of the second single stranded DNA fragment, or a ratio of the level of the second single stranded DNA fragment to the level of the first single stranded DNA fragment;   iv. comparing the ratio measured at step iii) with a ratio of predetermined corresponding reference values; and   v. administering one or more cancer treatments to a subject identified as having a a ratio that differs from the ratio of the predetermined reference values, wherein the one or more cancer treatments are selected from the group consisting of radiotherapy, chemotherapy and immunotherapy.   
     
     
         3 . A method for screening and treating a subject for a cancer, comprising the steps of:
 i. extracting the cell free nucleic acids from a sample obtained from the subject;   ii. denaturating the cell free nucleic acids to obtain single stranded DNA fragments;   iii. measuring a level of a first group of single stranded DNA fragments on a specific range having a length between 20 to 400 nucleotides;   iv. measuring a level of a second group of single stranded DNA fragments on a specific range having a length between 20 to 400 nucleotides;   v. calculating the ratio of the level measured at step iii) to the level at step iv) or alternatively the ratio of the level determined at step iv) to the level measured at step iii;   vi. comparing the ratio measured at step v) with a ratio of predetermined corresponding reference values;   vii. concluding that the subject suffers from a cancer when the ratio determined at step v) differs from the predetermined corresponding reference value; and   viii. administering one or more cancer treatments to a subject identified as having a a ratio that differs from the ratio of the predetermined reference values, wherein the one or more cancer treatments are selected from the group consisting of radiotherapy, chemotherapy and immunotherapy.   
     
     
         4 . A method for screening and treating a subject for a cancer, comprising the steps of:
 i. extracting cell free nucleic acids from a sample obtained from the subject;   ii. denaturating the cell free nucleic acids to obtain single stranded DNA fragments;   iii. measuring a level of a group of single stranded DNA fragments on a specific range having a length between 20 to 400 nucleotides;   iv. measuring a level of one single stranded DNA fragment having a length between 20 to 400 nucleotides;   v. calculating a ratio of the level measured at step iii) to the level measured at step iv) or a ratio of the level measured at step iv) to the level measured at step iii);   vi. comparing the ratio determined at step v) with a ratio of predetermined corresponding reference value;   vii. concluding that the subject suffers from a cancer when the ratio determined at step v) differs from the ratio of predetermined corresponding reference value; and   viii. administering one or more cancer treatments to a subject identified as having a ratio determined at step v) that differs from the ratio of corresponding predetermined reference values, wherein the one or more cancer treatments are selected from the group consisting of radiotherapy, chemotherapy and immunotherapy.   
     
     
         5 . The method according to  claim 1 , wherein the single stranded DNA fragment can have a length of 20; 21; 22; 23; 24; 25; 26; 27; 28; 29; 30; 31; 32; 33; 34; 35; 36; 37; 38; 39; 40; 41; 42; 43; 44; 45; 46; 47; 48; 49; 50; 51; 52; 53; 54; 55; 56; 57; 58; 59; 60; 61; 62; 63; 64; 65; 66; 67; 68; 69; 70; 71; 72; 73; 74; 75; 76; 77; 78; 79; 80; 81; 82; 83; 84; 85; 86; 87; 88; 89; 90; 91; 92; 93; 94; 95; 96; 97; 98; 99; 100; 101; 102; 103; 104; 105; 106; 107; 108; 109; 110; 111; 112; 113; 114; 115; 116; 117; 118; 119; 120; 121; 122; 123; 124; 125; 126; 127; 128; 129; 130; 131; 132; 133; 134; 135; 136; 137; 138; 139; 140; 141; 142; 143; 144; 145, 146; 147; 148; 149; 150; 151; 152; 153; 154; 155; 156; 157; 158; 159; 160; 161; 162; 163; 164; 165; 166; 167; 168; 169; 170; 171; 172; 173; 174; 175; 176; 177; 178; 179; 180; 181; 182; 183; 184; 185; 186; 187; 188; 189; 190; 191; 192; 193; 194; 195; 196; 197; 198; 199; 200; 201; 202; 203; 204; 205; 206; 207; 208; 209; 210; 211; 212; 213; 214; 215; 216; 217; 218; 219; 220; 221; 222; 223; 224; 225; 226; 227; 228; 229; 230; 231; 232; 233; 234; 235; 236; 237; 238; 239; 240; 241; 242; 243; 244; 245; 246; 247; 248, 249; 250; 251; 252; 253; 256; 257; 258; 259; 260; 261; 262; 263; 264; 265; 266; 267; 268; 269; 270; 271; 272; 273; 274; 275; 276; 277; 278; 279; 280; 281; 282; 283; 284; 285; 286; 287; 288; 289; 290; 291; 292; 293; 294; 295; 296; 297; 298; 299; 300; 301; 302; 303; 304; 305; 306; 307; 308; 309; 310; 311; 312; 313; 314; 315; 316; 317; 318; 319; 320; 321; 322; 323; 324; 325; 326; 327; 328; 329; 330; 331; 332; 333; 334; 335; 336; 337; 338; 339; 340; 341; 342; 343; 344; 345; 346; 347; 348; 349; 350; 351; 352; 353; 354; 355; 356; 357; 358; 359; 360; 361; 362; 363; 364; 365; 366; 367; 368; 369; 370; 371; 372; 373; 374; 375; 376; 377; 378; 379; 380; 381; 382; 383; 384; 385; 386; 387; 388; 389; 390; 391; 392; 393; 394; 395; 396; 397; 398; 399 or 400 nucleotides. 
     
     
         6 . The method according to  claim 1 , wherein the sample is blood, ascites, urine, amniotic fluid, feces, saliva or cerebrospinal fluids. 
     
     
         7 . The method of  claim 1 , further comprising the steps of
 i. applying the method according to  claim 1  before the treatment;   ii. applying the method according to  claim 1  after the treatment;   iii. comparing the level(s) determined at step i) with the level(s) determined at step and;   iv. concluding that the subject suffers from a cancer when the level(s) determined at step i) differ from the level(s) determined at step ii).   
     
     
         8 . The method of  claim 1 , further comprising the steps of:
 i. applying the method according to  claim 1  after the treatment;   ii. comparing the level(s) measured at step i) with a predetermined reference value and;   iii. concluding that the subject has a relapse when the level(s) measured at step i) differ from the predetermined reference value.