Chromosome conformation markers of autism spectrum disorder

1 . A process for determining an autism spectrum disorder (ASD) status in a human individual comprising detecting in the human individual the presence or absence of one or more of the chromosome interactions (i) to (xx) listed below:

(i) the chromosome interaction on chromosome 7 formed by the first region of chromosome position number 106136913 to 106136942 and the second region of chromosome position number 106155637 to 106155666,

(ii) the chromosome interaction on chromosome 2 formed by the first region of chromosome position number 209638896 to 209638925 and the second region of chromosome position number 209692609 to 209692638,

(iii) the chromosome interaction on chromosome 2 formed by the first region of chromosome position number 39609951 to 39609980 and the second region of chromosome position number 39623227 to 39623256,

(iv) the chromosome interaction on chromosome 6 formed by the first region of chromosome position number 46267217 to 46267246 and the second region of chromosome position number 46295957 to 46295986,

(v) the chromosome interaction on chromosome 3 formed by the first region of chromosome position number 120809117 to 120809146 and the second region of chromosome position number 120844724 to 120844753,

(vi) the chromosome interaction on chromosome 10 formed by the first region of chromosome position number 3161201 to 3161230 and the second region of chromosome position number 3210552 to 3210581,

(vii) the chromosome interaction on chromosome 2 formed by the first region of chromosome position number 198099688 to 198099717 and the second region of chromosome position number 198137326 to 198137355,

(viii) the chromosome interaction on chromosome 12 formed by the first region of chromosome position number 30144612 to 30144641 and the second region of chromosome position number 30181631 to 30181660,

(ix) the chromosome interaction on chromosome 19 formed by the first region of chromosome position number 52224154 to 52224183 and the second region of chromosome position number 52267683 to 52267712,

(x) the chromosome interaction on chromosome 6 formed by the first region of chromosome position number 157189220 to 157189249 and the second region of chromosome position number 157240029 to 157240058,

(xi) the chromosome interaction on chromosome 7 formed by the first region of chromosome position number 106136913 to 106136942 and the second region of chromosome position number 106183994 to 106184023,

(xii) the chromosome interaction on chromosome 21 formed by the first region of chromosome position number 17087460 to 17087489 and the second region of chromosome position number 17114098 to 17114127,

(xiii) the chromosome interaction on chromosome 10 formed by the first region of chromosome position number 106496979 to 106497008 and the second region of chromosome position number 106538148 to 106538177,

(xiv) the chromosome interaction on chromosome 8 formed by the first region of chromosome position number 31178906 to 31178935 and the second region of chromosome position number 31205591 to 31205620,

(xv) the chromosome interaction on chromosome 13 formed by the first region of chromosome position number 34433098 to 34433127 and the second region of chromosome position number 34463900 to 34463929,

(xvi) the chromosome interaction on chromosome 5 formed by the first region of chromosome position number 149610434 to 149610463 and the second region of chromosome position number 149663577 to 149663606,

(xvii) the chromosome interaction on chromosome 3 formed by the first region of chromosome position number 43042541 to 43042570 and the second region of chromosome position number 43075798 to 43075827,

(xviii) the chromosome interaction on chromosome 14 formed by the first region of chromosome position number 99794537 to 99794566 and the second region of chromosome position number 99818383 to 99818412,

(xix) the chromosome interaction on chromosome 7 formed by the first region of chromosome position number 22368714 to 22368743 and the second region of chromosome position number 22401548 to 22401577,

(xx) the chromosome interaction on chromosome 18 formed by the first region of chromosome position number 58202024 to 58202053 and the second region of chromosome position number 58217905 to 58217934 wherein the presence of any of the chromosome interactions (i) to (xx) is associated with ASD;

wherein detection of the presence or absence of each chromosome interaction is by a process comprising the steps of:

(a) cross-linking of chromosome DNA regions of the human individual which have come together in a chromosome interaction,

(b) subjecting the cross-linked DNA regions to cleavage,

(c) ligating the cross-linked cleaved DNA ends to form ligated DNA, and

(d) detecting the presence or absence of the ligated DNA corresponding to each chromosome interaction to thereby determine the presence or absence of each chromosome interaction;

wherein detecting the presence or absence of the ligated DNA is by quantitative PCR (qPCR) which uses primers capable of amplifying the ligated DNA and a probe which binds the ligation site during the PCR reaction, wherein said probe comprises sequence which is complementary to sequence from each of the chromosome regions that have come together in the chromosome interaction.

2 . The process according to claim 1 , wherein the presence or absence of at least 1, 5, 8 or 10 of the chromosome interactions (i) to (xx) is determined.

3 . The process according to claim 1 , wherein the probe comprises:

a fluorophore covalently attached to the 5′ end of the probe, and/or

a quencher covalently attached to the 3′ end of the probe.

4 . The process according to claim 1 , wherein the individual has been preselected based on a physical characteristic, risk factor or symptom.

5 . The process according to claim 4 , wherein the individual has been preselected based on having a symptom of, or risk factor for: autistic disorder, childhood autism, Asperger's syndrome, PDD-NOS (Pervasive Development Disorder), childhood disintegrative disorder or addiction.