Herbal and Botanical

All Drugs and Chemicals

Cola

The group is to include at least 1000 individuals who are at high risk for the development of cancer. Risk is assessed through the completion of a clinical history questionnaire. Examples of such subjects include those with known hereditary cancer syndrome pathogenic variants without a diagnosis of cancer, with significant family history of breast, ovarian, colon, or lung cancer or melanoma, or another strong history of cancer but no prior molecular diagnosis, heavy smokers or those exposed to carcinogens and mutagens. The individuals who meet criteria for inclusion will undergo cell-free DNA isolation and circulating-tumor DNA (ctDNA) analysis for the detection of genetic mutations associated with the possible development of a malignancy.

Cell-free DNA (cfDNA) is isolated from a blood plasma sample and tested for the presence of 96 specific well-described mutations in 9 cancer driver genes. The presence of more than 2 copies of a mutation may indicate the presence of a malignancy. Follow up with the subject's physician would be needed for an examination and any additional testing that the physician wants to perform to further assess for the development of cancer.

ctDNA Analysis for the Detection of Genetic Mutations

Glenn Braunstein, MD

Anja Kammesheidt, PhD

Pathway Genomics Corporation (Pathway Genomics), a San Diego, California company, is involved in the development and validation of new molecular diagnostic assays for the analysis of circulating tumor deoxyribonucleic acid (DNA) (ctDNA) found in the plasma-derived DNA (cell-free DNA or cfDNA) in order to identify specific variants (mutations) in cancer driver genes. The purpose of testing for mutations in ctDNA is to detect and monitor cancer. All cells shed DNA into the bloodstream. Finding cancer-associated mutations in the cfDNA may lead to early detection of cancer in an otherwise apparently healthy (i.e. asymptomatic) individual or may allow the healthcare provider to more effectively monitor and treat a known cancer patient. The analysis is performed using a polymerase chain reaction (PCR)-based methodology where oligonucleotides are designed to target specific mutations in designated genes of interest followed by next generation deep sequencing of the amplified targets. Evaluation of the performance of these assays for screening for cancer in asymptomatic subjects is essential for the clinical validation of the use of these assays. The specific aim of this protocol is to obtain relevant human blood samples from individual subjects at higher than average risk for the development of cancer due to age, heredity, or environmental or toxic exposures for use in the statistical analysis of this method as an adjunct screening test for the potential presence of cancer.

The objectives of this study are to obtain human blood samples from asymptomatic subjects who have never been diagnosed with cancer, but who may be at increased risk for cancer due to heredity, exposures, age, or family history to assess the validity of screening healthy but at risk patients for cancer via analysis of ctDNA.

Specifically, the blood specimens will be collected from individuals who have responded to a self-administered health questionnaire that screens for higher risk of contracting cancer. Each participant will be asked to provide a 30 ml blood sample to be drawn by a primary care provider (PCP) or licensed phlebotomist. The specimens collected during the study may also be used in the research and development of new or modified molecular genetics assays. The results of these studies will be used to further the understanding of the use of ctDNA for the detection and monitoring of cancer in humans.

The blood samples are collected in blood collection tubes (BCT) called Cell-Free DNA BCT® manufactured by Streck and intended for collection, stabilization and transportation of cell-free plasma DNA. This device also stabilizes and preserves cellular genomic DNA present in nucleated blood cells and circulating epithelial cells (tumor cells) found in whole blood. This product has not been cleared by the U.S. Food and Drug Administration for In Vitro Diagnostic use and is labeled by Streck for research use only. Under the Clinical Laboratory Improvement Amendments (CLIA) regulations, laboratories are authorized to validate and use, as part of a laboratory-developed test (LDT), devices that have not been cleared or approved by the FDA. Pathway Genomics validated the CancerInterceptTM Detect molecular analysis system with the Streck tubes, in accordance with CLIA.

Once the specimen has been collected and sent to Pathway by the physician or the phlebotomist who collects the samples, all other processing and testing are conducted by Pathway laboratory personnel. The analysis begins with the separation of the plasma from the rest of the blood sample. cfDNA will then be isolated from each sample. The quantity of cfDNA is measured and then the sample is amplified via PCR for next generation sequencing. The results of the sequencing will then be analyzed for the presence of one or more of the 96 mutations analyzed in this assay. The data are then reviewed and a report will be generated.

Whole blood will be obtained, the plasma sample separated for the isolation of cell-free DNA, and the sample that may be stored will be excess plasma as well as potentially DNA from the buffy coat.

Utility of Plasma Circulating Tumor DNA (ctDNA) in Asymptomatic Subjects for the Detection of Neoplastic Disease

A cohort of 1000 or more individuals who are at high risk for the development of cancer will be tested for the presence of 96 well-described mutations in 9 cancer driver genes via ctDNA analysis. The number of individuals with one or more of the 96 assayed mutations will be assessed.

Among the cohort of subjects enrolled in the study in whom one or more of the 96 ctDNA mutations are detected, the number of copies per analyzed plasma sample will be calculated.

Within the samples found to contain one or more ctDNA mutation, the percentage of ctDNA within the total amount of cfDNA will be calculated.

The 1000 or more individuals in the study will be followed for 1 to 5 years to assess for the development of a malignancy. Special attention will be paid to the cohort who have initial assays indicating the presence of ctDNA. The subjects may be retested over time to show changing levels of ctDNA. Their own physicians will guide any follow up studies such as imaging or other laboratory testing. The test is designed as a means of case finding for cancer among individuals with high risk for development of cancer.

Pathway Genomics

Infections

All Conditions

Symptoms and General Pathology

Immune System Diseases

Urinary Tract, Sexual Organs, and Pregnancy Conditions

Rare Diseases

Communicable Diseases

Hypersensitivity

Virus Diseases

Papillomavirus Infections

Sexually Transmitted Diseases

Sexually Transmitted Diseases, Viral

DNA Virus Infections

Tumor Virus Infections

Genital Diseases

Urogenital Diseases

Disease Attributes

Cervical Intraepithelial Neoplasia

The Adjunct study will evaluate APTIMA HPV Assay clinical performance for detecting high-risk HPV types in female subjects 30+ years of age with negative (NILM) cytology results from routine Pap testing. This will be accomplished by evaluating the assay performance compared to known cervical disease status at baseline and after a 3-year follow-up period. A comparator FDA-Approved HPV DNA test is reported.

The ASC-US study will evaluate the APTIMA HPV Assay clinical performance for detecting high-risk HPV types in subjects with ASC-US Pap test results from routine Pap testing and known cervical disease status (based on colposcopic biopsy results). A comparator FDA-Approved HPV DNA test is reported. There is no follow-up period.

The APTIMA HPV Assay is an in vitro nucleic acid amplification test (NAAT) that qualitatively detects human papillomavirus (HPV) E6/E7 messenger RNA (mRNA) from 14 HPV types (types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) that are associated with cervical cancer ("high-risk types"). The assay cannot determine the specific high-risk HPV type(s) present and does not cross-react with 5 HPV types that are considered non-oncogenic (not associated with cervical cancer; types 6, 11, 42, 43, and 44).

APTIMA HPV Assay

A FDA-Approved HPV DNA Test is used as the comparator assay.

FDA-Approved HPV DNA Test

Jennifer L Reid, PhD

The purpose of this study is to provide data on the performance of the APTIMA HPV Assay using the TIGRIS System in detecting HPV types that may cause cervical cancer.

The primary objective of the clinical trial is to evaluate the APTIMA HPV Assay, using the TIGRIS System, in cervical cancer screening programs. This will be achieved by determining the performance of the assay for detecting high-risk human papillomavirus (HPV) types in women with known cervical disease status. The assay will be evaluated in sample populations of women with ASC-US Pap test results ("ASC-US results") and women 30 years of age or older ("30+ years of age") with negative (NILM) cytology results.

Clinical Evaluation of the APTIMA® HPV Assay Using the TIGRIS® System

Clinical Evaluation of the APTIMA® HPV Assay on the TIGRIS® DTS® System in Women With ASC-US Pap Test Results and in Women 30 Years of Age or Older With Negative Pap Test Results Using ThinPrep Pap Test Specimens

Adjunct 30+ yrs. Population: Aptima HPV Assay Performance for Detecting CIN2+: Compare Clinical Performance of the Aptima HPV Assay to a FDA-Approved HPV Assay for Detecting CIN2+

Adjunct Study Arm: 30+ yrs. Population: FDA-Approved HPV DNA Assay Performance for Detecting CIN2+: Compare Clinical Performance of the Aptima HPV Assay to a FDA-Approved HPV Assay for Detecting CIN2+

ASC-US Study Arm: 21+ yrs. Population: Aptima HPV assay performance on Tigris System for detecting CIN2+ (All Biopsies)

ASC_US Study Arm: 21+ yrs. Population for Detecting CIN2+ (All Biopsies): FDA-Approved HPV DNA Assay

Gen-Probe, Incorporated

2 years for recruitment for Adjunct and ACS-US Arms with a 3 years follow-up period for the Adjunct Arm

The Adjunct study will evaluate APTIMA HPV Assay performance for detecting high-risk HPV types in female subjects 30+ years of age with negative (NILM) cytology results from routine Pap testing. This will be accomplished by evaluating the assay performance compared to known cervical disease status at baseline and after a 3-year follow-up period.

APTIMA HPV Assay: The APTIMA HPV Assay is an in vitro nucleic acid amplification test (NAAT) that qualitatively detects human papillomavirus (HPV) E6/E7 messenger RNA (mRNA) from 14 HPV types (types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) that are associated with cervical cancer ("high-risk types"). The assay cannot determine the specific high-risk HPV type(s) present and does not cross-react with 5 HPV types that are considered non-oncogenic (not associated with cervical cancer; types 6, 11, 42, 43, and 44).

Adjunct (i.e. Normal Pap)

The ASC-US study will determine the sensitivity and specificity of the APTIMA HPV Assay for detecting high-risk HPV types in subjects with ASC-US Pap test results from routine Pap testing and known cervical disease status (based on colposcopic biopsy results).

APTIMA HPV Assay: The APTIMA HPV Assay is an in vitro nucleic acid amplification test (NAAT) that qualitatively detects human papillomavirus (HPV) E6/E7 messenger RNA (mRNA) from 14 HPV types (types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) that are associated with cervical cancer ("high-risk types"). The assay cannot determine the specific high-risk HPV type(s) present and does not cross-react with 5 HPV types that are considered non-oncogenic (not associated with cervical cancer; types 6, 11, 42, 43, and 44).

ASC-US

Total

Age, Continuous

21 - <30 years

30 - <40 years

40+ years

Age, Customized

Gender

Ethnicity (NIH/OMB)

Race (NIH/OMB)

United States

Region of Enrollment

Vice President Clinical Affairs

Assay Positive, CIN2+

Assay Negative, CIN2+

Assay Positive, No Disease

Assay Negative, No Disease

The Adjunct study will evaluate APTIMA HPV Assay clinical performance for detecting high-risk HPV types in female subjects 30+ years of age with negative (NILM) cytology results from routine Pap testing. This will be accomplished by evaluating the assay performance compared to known cervical disease status at baseline and after a 3-year follow-up period.

APTIMA HPV Assay: The APTIMA HPV Assay is an in vitro nucleic acid amplification test (NAAT) that qualitatively detects human papillomavirus (HPV) E6/E7 messenger RNA (mRNA) from 14 HPV types (types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) that are associated with cervical cancer ("high-risk types"). The assay cannot determine the specific high-risk HPV type(s) present and does not cross-react with 5 HPV types that are considered non-oncogenic (not associated with cervical cancer; types 6, 11, 42, 43, and 44).

Adjunct Study Arm: Compare Assay Performance for Aptima HPV Assay to a FDA-Approved HPV Assay for Detecting CIN2+

A FDA-Approved HPV DNA Test is the comparator assay,

FDA-Approved DNA Test

18 women with Aptima HPV results did not have FDA-Approved DNA test results due to insufficient volume of the cytology specimen for a N of 801 compared to a N of 819 for the Aptima HPV assay results.

Adjunct Study Arm: Compare Assay Performance for FDA-Approved HPV DNA Assay to a FDA-Approved HPV Assay for Detecting CIN2+

APTIMA HPV Assay Performed on the Tigris System

ASC-US Study Arm: Aptima HPV Assay Performance for Detecting CIN2+ (All Biopsies)

74 women with Aptima HPV assay results did not have FDA-Approved HPV DNA test results primarily due to insufficient volume of the cytology specimen for an N of 865 results for the FDA-Approved HPV DNA assay compared to 939 results for the Aptima HPV assay.

ASC-US Study Arm: FDA-Approved HPV DNA Assay Performance for Detecting CIN2+ (All Biopsies)

The ASC-US study will determine the sensitivity and specificity of the APTIMA HPV Assay for detecting high-risk HPV types in subjects with ASC-US Pap test results from routine Pap testing and known cervical disease status (based on colposcopic biopsy results).

APTIMA HPV Assay: The APTIMA HPV Assay is an in vitro nucleic acid amplification test (NAAT) that qualitatively detects human papillomavirus (HPV) E6/E7 messenger RNA (mRNA) from 14 HPV types (types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) that are associated with cervical cancer ("high-risk types"). The assay cannot determine the specific high-risk HPV type(s) present and does not cross-react with 5 HPV types that are considered non-oncogenic (not associated with cervical cancer; types 6, 11, 42, 43, and 44).

There is no follow-up period for the ASC-US Arm of the study, only for the Adjunct ARM has a three (3) year follow-up period.

Study title	NCT ID	Conditions	Interventions	Eligibility	Organization
Utility of Plasma Circulating Tumor DNA (ctDNA) in Asymptomatic Subjects for the Detection of Neoplastic Disease	NCT02612350	Mutation Neoplasms	ctDNA Analysis ...	18 Years -	Pathway Genomics
Utility of Plasma Circulating Tumor DNA (ctDNA) in Asymptomatic Subjects for the Detection of Neoplastic Disease	NCT02612350	Mutation Neoplasms	ctDNA Analysis ...	18 Years -	Pathway Genomics
Clinical Evaluation of the APTIMA® HPV Assay Using the TIGRIS® System	NCT00973362	Human Papilloma...	APTIMA HPV Assa... FDA-Approved HP...	21 Years -	Gen-Probe, Incorporated

Spots Global Cancer Trial Database for relative risk