Method for identifying or detecting genomic rearrangements in a biological sample

Abstract

A method for detection, visualization and/or comparison of polynucleotide sequences of interest using specially designed sets of long and short probes that enhance resolution and simplify visualization and detection. Probe compositions useful for practicing this method and procedures for identifying useful probes and probe combinations. These methods are useful for the detection of genomic rearrangements, especially those associated with various diseases, disorders and conditions including cancer or for assessment of genomic rearrangements associated with therapy. The probe compositions may be used in kits for detection of genetic rearrangements or in companion diagnostic products or kits, such as kits for the diagnosis or assessment of predisposition to cancer such as colorectal cancer.

1 - 48 . (canceled) 
     
     
         49 . A kit comprising a set of short probes hybridizing specifically on the MSH2 gene or on the MLH1 gene, and suitable for the detection of rearrangements within said MSH2 gene or MLH1 gene, wherein at least one short probe comprises a label for detection and wherein, for each of detection,
 (i) the set of short probes comprises a set of probes that taken together hybridize to a continuous stretch of more than 12 kb of the MSH2 gene or of the MLH1 gene; or   (ii) the kit further comprises a set of long probes, wherein the long probes bind to sequences outside the MSH2 gene or the MLH1 gene and do not overlap the short probe sequences,   wherein the short probe sequence(s) specific of the MSH2 gene are obtained by amplification on human genomic DNA using primer pairs, wherein the primer pairs are selected from the group consisting of the sequences of SEQ ID NO: 21 and SEQ ID NO: 22, the sequences of SEQ ID NO: 23 and SEQ ID NO: 24, the sequences of SEQ ID NO: 25 and SEQ ID NO: 26, the sequences of SEQ ID NO: 27 and SEQ ID NO: 28, the sequences of SEQ ID NO: 29 and SEQ ID NO: 30, the sequences of SEQ ID NO: 31 and SEQ ID NO: 32, the sequences of SEQ ID NO: 33 and SEQ ID NO: 34, the sequences of SEQ ID NO: 35 and SEQ ID NO: 36, the sequences of SEQ ID NO: 37 and SEQ ID NO: 38, the sequences of SEQ ID NO: 39 and SEQ ID NO: 40, the sequences of SEQ ID NO: 41 and SEQ ID NO: 42, the sequences of SEQ ID NO: 43 and SEQ ID NO: 44, the sequences of SEQ ID NO: 45 and SEQ ID NO: 46, the sequences of SEQ ID NO: 47 and SEQ ID NO: 48, the sequences of SEQ ID NO: 49 and SEQ ID NO: 50, the sequences of SEQ ID NO: 51 and SEQ ID NO: 52, the sequences of SEQ ID NO: 53 and SEQ ID NO: 54, the sequences of SEQ ID NO: 55 and SEQ ID NO: 56, the sequences of SEQ ID NO: 57 and SEQ ID NO: 58, the sequences of SEQ ID NO: 59 and SEQ ID NO: 60, the sequences of SEQ ID NO: 163 and SEQ ID NO: 164, the sequences of SEQ ID NO: 165 and SEQ ID NO: 166, the sequences of SEQ ID NO: 167 and SEQ ID NO: 168, the sequences of SEQ ID NO: 169 and SEQ ID NO: 170, the sequences of SEQ ID NO: 171 and SEQ ID NO: 172, the sequences of SEQ ID NO: 185 and SEQ ID NO: 186, the sequences of SEQ ID NO: 187 and SEQ ID NO: 188, the sequences of SEQ ID NO: 189 and SEQ ID NO: 190, the sequences of SEQ ID NO: 191 and SEQ ID NO: 192, the sequences of SEQ ID NO: 193 and SEQ ID NO: 194, the sequences of SEQ ID NO: 195 and SEQ ID NO: 196, the sequences of SEQ ID NO: 197 and SEQ ID NO: 198, the sequences of SEQ ID NO: 199 and SEQ ID NO: 200, and the sequences of SEQ ID NO: 201 and SEQ ID NO: 202; and   wherein the short probe sequence(s) specific of the MLH I gene are obtained by amplification on human genomic DNA using primer pairs, wherein the primer pairs are selected from the group consisting of the sequences of SEQ ID NO: 95 and SEQ ID NO: 96, the sequences of SEQ ID NO: 97 and SEQ ID NO: 98, the sequences of SEQ ID NO: 99 and SEQ ID NO: 100, the sequences of SEQ ID NO: 101 and SEQ ID NO: 102, the sequences of SEQ ID NO: 103 and SEQ ID NO: 104, the sequences of SEQ ID NO: 105 and SEQ ID NO: 106, the sequences of SEQ ID NO: 107 and SEQ ID NO: 108, the sequences of SEQ ID NO: 109 and SEQ ID NO: 110, the sequences of SEQ ID NO: 111 and SEQ ID NO: 112, the sequences of SEQ ID NO: 113 and SEQ ID NO: 114, the sequences of SEQ ID NO: 115 and SEQ ID NO: 116, the sequences of SEQ ID NO: 117 and SEQ ID NO: 118, the sequences of SEQ ID NO: 119 and SEQ ID NO: 120, the sequences of SEQ ID NO: 121 and SEQ ID NO: 122, the sequences of SEQ ID NO: 227 and SEQ ID NO: 228, the sequences of SEQ ID NO: 229 and SEQ ID NO: 230, the sequences of SEQ ID NO: 231 and SEQ ID NO: 232, the sequences of SEQ ID NO: 233 and SEQ ID NO: 234, the sequences of SEQ ID NO: 235 and SEQ ID NO: 236, the sequences of SEQ ID NO: 237 and SEQ ID NO: 238, the sequences of SEQ ID NO: 239 and SEQ ID NO: 240, the sequences of SEQ ID NO: 241 and SEQ ID NO: 242, the sequences of SEQ ID NO: 243 and SEQ ID NO: 244, the sequences of SEQ ID NO: 245 and SEQ ID NO: 246, and the sequences of SEQ ID NO: 247 and SEQ ID NO: 248; and   wherein the long probe sequence(s) specific of the MSH2 gene are obtained by amplification on human genomic DNA using primer pairs, wherein the primer pairs are selected from the group consisting of the sequences of SEQ ID NO: 61 and SEQ ID NO: 62, the sequences of SEQ ID NO: 63 and SEQ ID NO: 64, the sequences of SEQ ID NO: 65 and SEQ ID NO: 66, the sequences of SEQ ID NO: 67 and SEQ ID NO: 68, the sequences of SEQ ID NO: 69 and SEQ ID NO: 70, the sequences of SEQ ID NO: 71 and SEQ ID NO: 72, the sequences of SEQ ID NO: 73 and SEQ ID NO: 74, and the sequences of SEQ ID NO: 75 and SEQ ID NO: 76; and   wherein the long probe sequence(s) specific of the MLH I gene are obtained by amplification on human genomic DNA using primer pairs, wherein the primer pairs are selected from the group consisting of the sequences of SEQ ID NO: 123 and SEQ ID NO:   124, the sequences of SEQ ID NO: 125 and SEQ ID NO: 126, the sequences of SEQ ID NO:   127 and SEQ ID NO: 128, the sequences of SEQ ID NO: 129 and SEQ ID NO: 130, the sequences of SEQ ID NO: 131 and SEQ ID NO: 132, the sequences of SEQ ID NO: 133 and SEQ ID NO: 134, the sequences of SEQ ID NO: 135 and SEQ ID NO: 136, and the sequences of SEQ ID NO: 137 and SEQ ID NO: 138.   
     
     
         50 . The kit according to  claim 49  for the detection of genomic rearrangements associated with a condition selected from the group consisting of: colorectal cancer or genetic predisposition to colorectal cancer, breast cancer or genetic predisposition to breast cancer, ovarian cancer or genetic predisposition to ovarian cancer, and lung cancer or genetic predisposition to lung cancer. 
     
     
         51 . The kit according to  claim 49 , wherein the kit comprises a set of long probes, wherein the long probes bind to sequences outside the MSH2 gene or the MLH1 gene and do not overlap the short probe sequences. 
     
     
         52 . The kit according to  claim 49 , wherein different components of the probe sets are tagged with different labels for detection. 
     
     
         53 . The kit according to  claim 49 , wherein the set of short probes comprises a set of probes that taken together hybridize to a continuous stretch of more than 12 kb of the MSH2 gene or of the MLH1 gene and at least one short probe comprises a label for detection. 
     
     
         54 . The kit according to  claim 49 , wherein the short probe sequences hybridize specifically on the MSH2 gene. 
     
     
         55 . The kit according to  claim 49 , wherein the short probe sequences hybridize specifically on the MLH1 gene. 
     
     
         56 . The kit according to  claim 49 , wherein the long probe sequences hybridize specifically on the MSH2 gene. 
     
     
         57 . The kit according to  claim 49 , wherein the long probe sequences hybridize specifically on the MLH1 gene.