JPWO2020176620A5

JPWO2020176620A5 -

Info

Publication number: JPWO2020176620A5
Application number: JP2021550012A
Authority: JP
Publication date: 2023-03-07

Claims

1. A method for identifying a first cancer condition and a second cancer condition in a human subject, wherein the first cancer condition is cervical cancer associated with infection with the human papillomavirus (HPV) oncogenic virus; or head and neck cancer associated with infection by HPV, wherein said second cancer condition is cervical cancer associated with HPV-free conditions or head and neck cancer associated with HPV-free conditions , said method comprising: ,
(A) obtaining a dataset for the subject, the dataset comprising a plurality of abundance values from the subject;
each respective abundance value in the plurality of abundance values quantifies the level of expression of a corresponding gene in a plurality of genes in cancerous tissue from the subject;
obtaining, wherein the plurality of genes comprises at least 10 genes selected from the genes listed in Table 3;
(B) inputting the dataset into a classifier trained to distinguish at least the first cancer state and the second cancer state based on the abundance values of the plurality of genes; A method, including

2. The method of claim 1 , wherein said plurality of genes comprises at least 20 genes selected from the genes listed in Table 3.

2. The method of claim 1 , wherein said plurality of genes includes at least all 24 of the genes listed in Table 3.

4. The method of any one of claims 1-3, wherein the plurality of genes comprises 300 genes or less.

5. The method of any one of claims 1-4 , further comprising determining the plurality of abundance values by RNA sequencing of a sample of the cancerous tissue from the human cancer patient.

6. The data set of any one of claims 1-5 , wherein the dataset further comprises variant allele counts for one or more alleles at one or more loci in the genome of the cancerous tissue from the subject. The method described in section.

7. The method of claim 6 , wherein said one or more mutant alleles are selected from mutant alleles in the TP53 (ENSG00000141510) or CDKN2A (ENSG00000147889) genes.

wherein said classifier is a logistic regression algorithm, a neural network algorithm, a convolutional neural network algorithm, a support vector machine algorithm, a Naive Bayes algorithm, a nearest neighbor algorithm, a boosted tree algorithm, a random forest algorithm, a decision tree algorithm, or a clustering algorithm; Item 8. The method according to any one of Items 1 to 7 .

A first therapy tailored for the treatment of cervical cancer or head and neck cancer associated with HPV infection if the results of the classifier indicate that the human cancer patient is infected with the HPV oncogenic virus. and
A second therapy tailored for the treatment of cervical or head and neck cancer not associated with HPV infection if the results of the classifier indicate that the human cancer patient is free of HPV oncogenic virus. to assign
The method of any one of claims 1-8, further comprising allocating therapy for cervical cancer or head and neck cancer by.

10. The method of claim 9 , wherein said first therapy tailored for the treatment of cervical cancer associated with HPV infection is therapeutic vaccine or adoptive cell therapy .

11. The method of claim 9 or 10 , wherein said second therapy adjusted for treatment of cervical cancer not associated with HPV infection is chemotherapy.

10. The method of claim 9 , wherein said first therapy adjusted for the treatment of head and neck cancer associated with HPV infection is a therapeutic vaccine , immune checkpoint inhibitor, or PI3K inhibitor .

13. The method of claim 9 or 12 , wherein said second therapy adjusted for treatment of head and neck cancer not associated with HPV infection is chemotherapy.

14. The method of claim 11 or 13 , wherein said chemotherapy comprises administration of cisplatin.

15. The claim 14 , wherein said second therapy adjusted for treatment of cervical cancer further comprises co-administration of a second therapeutic agent selected from the group consisting of 5-fluorouracil, paclitaxel, and bevacizumab. the method of.

15. The method of claim 14 , wherein said second therapy adjusted for treatment of head and neck cancer further comprises concurrent radiotherapy or postoperative chemoradiation therapy.