Detection of chromosome interactions as indicative of amyotrophic lateral sclerosis

A process for selecting a human individual and treating the selected human individual, wherein the selected human individual is in need of therapy for amyotrophic lateral sclerosis (ALS), wherein selecting the human individual is by:

• detecting the absence of a first chromosome interaction,
• detecting the presence of a second chromosome interaction,
• detecting the presence of a third chromosome interaction,
• detecting the presence of a fourth chromosome interaction,
• detecting the presence of a fifth chromosome interaction,
• detecting the absence of a sixth chromosome interaction,
• detecting the absence of a seventh chromosome interaction,
• detecting the absence of an eighth chromosome interaction,
• detecting the presence of a ninth chromosome interaction,
• detecting the absence of a tenth chromosome interaction,
• detecting the absence of an eleventh chromosome interaction,
• detecting the absence of a twelfth chromosome interaction,
• detecting the presence of a thirteenth chromosome interaction,
• detecting the presence of a fourteenth chromosome interaction,
• detecting the presence of a fifteenth chromosome interaction,
• detecting the presence of a sixteenth chromosome interaction, and
• detecting the presence of a seventeenth chromosome interaction
• in a sample from the human individual;
• and treating the selected human individual for amyotrophic lateral sclerosis (ALS) by administering an agent which is therapeutic for amyotrophic lateral sclerosis (ALS);
• wherein said detecting comprises:
• (i) cross-linking of chromosome regions which have come together in a chromosome interaction;
• (ii) subjecting said cross-linked regions to cleavage to form cross-linked cleaved nucleic acid;
• (iii) ligating said cross-linked cleaved nucleic acid ends to form ligated nucleic acid;
• and
• (iv) detecting the presence or absence of the ligated nucleic acid;
• wherein:
• the ligated nucleic acid corresponding to the first chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 2)
• TCACCACACATCACCCCCTTGCTCCTCCTCGAGTCTTGGTGACCACAAC
• AGGGTGCCACC,
• the ligated nucleic acid corresponding to the second chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 3)
• GAGGTGGGTGAATCATGAGGTCAAGGGTTCGACAATAGTTGAGAATCTC
• CAACCACCTGG,
• the ligated nucleic acid corresponding to the third chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 4)
• GGCCTTATAGTCAGCTGATCAGGTGAAATCGATTGGTCCTTAGGATCAGC
• TACCATTTGC,
• the ligated nucleic acid corresponding to the fourth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 5)
• GAGGCAGGCGGATCACAAAGTCAAAAGATCGATAACTTCAATAATAGTTA
• CAGATGCAAA,
• the ligated nucleic acid corresponding to the fifth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 6)
• AGCACCATATCTGGGATGTAGCTATTGCTCGAGATTGCAGTGAGCTGTGA
• TCACACCTCT,
• the ligated nucleic acid corresponding to the sixth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 7)
• TCTTCCCTCTTTTTAAAACCACCATTCATCGACCCCACACATCCTGTGCC
• ACTCTACTGC,
• the ligated nucleic acid corresponding to the seventh chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 8)
• TAACCATTATGCATCACTAACATAGCATTCGATATGATATGCTCAGTTTA
• GTTAGGGAAA,
• the ligated nucleic acid corresponding to the eighth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 9)
• GGCTCAGGAAGAGAACTATTTGTCTCTTTCGACACGCACATGCAGGACAC
• TCACACGTAG,
• the ligated nucleic acid corresponding to the ninth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 10)
• GTTGGGTGGATCCCTTGAGCTCAGGAATTCGAAGAATGATTTTTCAGCCC
• GTGTGGAAGG,
• the ligated nucleic acid corresponding to the tenth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 11)
• ATCAAAAGAAAATAGATACTTGTCTTACTCGAGTTGAATAAAATCCTCAG
• CTTTCTGTCC,
• the ligated nucleic acid corresponding to the eleventh chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 12)
• AAAAGAAACTGTGAAAAGTTGTCACATTTCGATTAAATCCAAAAAGGTCT
• TCTATGAGGC,
• the ligated nucleic acid corresponding to the twelfth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 13)
• TTAAAAGTATAGTAGTTGGCATTAACATTCGACCTTTTTCTGTTTCAGTA
• ACCAACCCAG,
• the ligated nucleic acid corresponding to the thirteenth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 14)
• CATCAACTAATAGTTAAACATTATAATATCGACTGAAGACCTTTCATACT
• GTAAGATTCA,
• the ligated nucleic acid corresponding to the fourteenth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 15)
• CATCAACTAATAGTTAAACATTATAATATCGAGTCTGCAGTGAGCTGAGA
• TCACACTGCC,
• the ligated nucleic acid corresponding to the fifteenth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 16)
• TTATTCCTTTCCAAATAGTTAAAATTATTCGAAACTTTTAAGAATCAATA
• TAAAATTTCC,
• the ligated nucleic acid corresponding to the sixteenth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 17)
• CATAATTATAAATTAAAAAATGACACTATCGATTATGTCCAGTGTTTCTT
• GGTTGGTGTC,
• and
• the ligated nucleic acid corresponding to the seventeenth chromosome interaction is detected by the probe sequence
• (SEQ ID NO:
• 18)
• CAGAGCACTAAGATAGACTTCTAAGGTTTCGAGGCATATAGCTCCAGCTG
• TATTGAGGTA.