Methods for detecting human papillomavirus-assocated cancers

A method of identifying an individual with one or more human chromosomal abnormalities diagnostic or indicative of one or more types of human papillomavirus (HPV)-associated cancer, the method comprising:

• (a) hybridizing a probe set with genetic material from a sample that is obtained from an individual, wherein the sample comprises genetic material from cervical tissue and/or fluid thereof, wherein hybridizing comprises fluorescence in situ hybridization (FISH), and wherein the probe set consists of
• (i) a first probe that hybridizes selectively to 3q26, wherein the first probe comprises a probe preparation of seven different nick-translated clones corresponding to chromosome 3, clones 1-7 of Table 4,
• (ii) a second probe that hybridizes selectively to 5p15, wherein the second probe comprises a probe preparation of five different nick-translated clones corresponding to chromosome 5, clones 1-5 of Table 4,
• (iii) a third probe that hybridizes selectively to 20q13, wherein the third probe comprises a probe preparation of three different nick-translated clones corresponding to chromosome 20, clones 1-3 of Table 4, and
• (iv) a fourth probe that hybridizes selectively to cen7, wherein the fourth probe comprises a probe preparation of a nick-translated clone corresponding to chromosome 7, clone 1 of Table 4;
• and
• (b) analyzing the hybridization pattern of the probe set to the genetic material to determine the presence or absence in the sample of a gain of 3q, a gain of 5p, a gain of 20q, and a gain of cen7.

A method of identifying in a sample one or more human chromosomal abnormalities diagnostic or indicative of one or more types of HPV-associated precancer or cancer, the method comprising:

• (a) hybridizing a probe set with genetic material from the sample, wherein the sample is obtained from an individual and comprises genetic material from cervical tissue and/or fluid thereof, wherein hybridizing comprises fluorescence in situ hybridization (FISH), and wherein the probe set consists of
• (i) a first probe that hybridizes selectively to 3q26, wherein the first probe comprises a probe preparation of seven different nick-translated clones corresponding to chromosome 3, clones 1-7 of Table 4,
• (ii) a second probe that hybridizes selectively to 5p15, wherein the second probe comprises a probe preparation of five different nick-translated clones corresponding to chromosome 5, clones 1-5 of Table 4,
• (iii) a third probe that hybridizes selectively to 20q13, wherein the third probe comprises a probe preparation of three different nick-translated clones corresponding to chromosome 20, clones 1-3 of Table 4, and
• (iv) a fourth probe that hybridizes selectively to cen7, wherein the fourth probe comprises a probe preparation of a nick-translated clone corresponding to chromosome 7, clone 1 of Table 4;
• and
• (c) analyzing the hybridization pattern of the probe set to the genetic material to determine the presence or absence in the sample of a gain of 3q, a gain of 5p, a gain of 20q, and a gain of cen7.

A method of identifying in a sample one or more human chromosomal abnormalities, the method comprising:

• (a) hybridizing a probe set with genetic material from the sample, wherein the sample is obtained from an individual and comprises genetic material from human tissue and/or fluid thereof, wherein hybridizing comprises fluorescence in situ hybridization (FISH), and wherein the probe set consists of
• (i) a first probe that hybridizes selectively to 3q26, wherein the first probe comprises a probe preparation of seven different nick-translated clones corresponding to chromosome 3, clones 1-7 of Table 4,
• (ii) a second probe that hybridizes selectively to 5p15, wherein the second probe comprises a probe preparation of five different nick-translated clones corresponding to chromosome 5, clones 1-5 of Table 4,
• (iii) a third probe that hybridizes selectively to 20q13, wherein the third probe comprises a probe preparation of three different nick-translated clones corresponding to chromosome 20, clones 1-3 of Table 4, and
• (iv) a fourth probe that hybridizes selectively to cen7, wherein the fourth probe comprises a probe preparation of a nick-translated clone corresponding to chromosome 7, clone 1 of Table 4;
• and
• (c) analyzing the hybridization pattern of the probe set to the genetic material to determine the presence or absence in the sample of a gain of 3q, a gain of 5p, a gain of 20q, and a gain of cen7.