Epigenetic Biomarker for Osteosarcoma

November 8, 2017 updated by: Peking University People's Hospital

Indentifying Epigenetic Biomarkers From Peripheral Blood of Osteosarcoma Patients Based on hMe-Seal Technique

hMe-Seal is a low-input whole-genome cell-free 5hmC sequencing method based on selective chemical labeling. It uses β-glucosyltransferase (βGT) to selectively label 5hmC with a biotin via an azide-modified glucose for pull-down of 5hmC-containing DNA fragments for sequencing. After selectively constructing 5hmC library, highthroughput-sequencing will be performed on an Illumina Nextseq-500 instrument. By ways of Rawdata processing, differential loci between Osteosarcoma group and control group will be detected to indentify specific epigenetic biomarkers of Osteosarcoma.

Study Overview

Status

Unknown

Conditions

Detailed Description

The investigator want to enroll 100 osteosarcoma participants initially treated in Musculoskeletal Tumor Center of Peking University People's Hospital(PKUPH). All those participants will follow the chemo-protocol for osteosarcoma in PKUPH.8 ml of peripheral blood would be drawed before each cycle of chemotherapy for further analysis. After definitive surgery, participants will need to take 8ml of peripheral blood every 2 months for 6 months. A total of 6 times of blood drawing will need to be done.

In hMe-Seal approach, peripheral blood is collected into EDTA-coated Vacutainers. Plasma is collected from the blood samples after centrifugation at 1 600× g for 10 min at 4 °C and 16 000× g at 10 min at 4 °C. CfDNA is extracted using the Circulating Nucleic Acid Kit(QIAGEN). After that, cfDNA (1-10 ng) is end repaired, 3'-adenylated and ligated to DNA Barcodes using KAPA Hyper Prep Kit (Kapa Biosystems). Ligated DNA is incubated in a solution containing HEPES buffer, UDP-6-N3-Glc and βGT . After that, DBCO-PEG4-biotin is directly added to the reaction mixture. Next, DNA is purified by Micro Bio-Spin 30 Column (Bio-Rad). The purified DNA is incubated with M270 Streptavidin beads (Life Technologies) in specific buffer. The beads are subsequently undergone three 5-min washes each with four kinds of different buffers. All binding and washing are done at room temperature with gentle rotation. Beads are then resuspended in water and amplified with 16 cycles of PCR amplification. The PCR products are purified using AMPure XP beads. Pair-end 38bp sequencing is performed on the NextSeq-500 instrument.

Study Type

Observational

Enrollment (Anticipated)

100

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Locations

  • China
      • Beijing, China, 100044
        • Recruiting
        • Peking University People's Hospital

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

10 years and older (ADULT, OLDER_ADULT, CHILD)

Accepts Healthy Volunteers

No

Genders Eligible for Study

All

Sampling Method

Non-Probability Sample

Study Population

Biopsy proved high-grade osteosarcoma, who should be older than 10 years and could complete routine chemo-protocol for osteosarcoma, could get enrolled.

Description

Inclusion Criteria:

  • 1) histologically confirmed high-grade osteosarcoma;
  • 2) older than 10 yrs;
  • 3) initially treated in Musculoskeletal Tumor Center of Peking University People's Hospital;
  • 4) Serum samples are available;
  • 5) completed neo-adjuvant chemotherapy and at least 8 cycles of adjuvant chemotherapy;
  • 6) expected to live longer than 3 months with Eastern Cooperative Oncology Group performance status of 0 or 1;
  • 7) acceptable hematologic, hepatic, and renal function.

Exclusion Criteria:

  • 1) Serum samples are not qualified;
  • 2) Patients who could not complete neo-adjuvant chemotherapy or at least 4-month adjuvant chemotherapy;
  • 3) lost to follow-up.

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

Cohorts and Interventions

Group / Cohort
observation group
One group of participants are under observation. This trial has two phase. Phase I: 40 participants will be enrolled. Only if epigenetic cfDNA library has been built, investigators would move on to Phase II. Another 60 participants will be enrolled for further analysis.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Histologic response
Time Frame: 2 months
For osteosarcoma, tumor necrosis rate will be done for every participant. On pathologic examination, the surgical specimens were carefully studied and sectioned. This evaluation included establishing the gross extent of the tumor[26, 27] and noting its soft tissue component and lines of surgical resection[27]. An average of 10-20 histologic specimens were examined in each of the en bloc resections to delineate the extension of osteosarcoma up and down the marrow cavity and to study the effects of chemotherapy on the tumor (viable, partially, largely, or totally necrotic), which were then calculated as tumor necrosis rate as paper described.
2 months

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Objective Response Rate
Time Frame: 2 months
According to RECIST 1.1, participants who meet the criteria of complete response and partial response.
2 months
Progression-free survival
Time Frame: 2 years
Progression-free survival (PFS) will be calculated from the start of chemotherapy to first progression.
2 years
Overall survival
Time Frame: 5 years
Overall survival (OS) will be calculated from the start of chemotherapy to death.
5 years

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Peking University People's Hospital

Collaborators

Peking University
Northwestern University
University of Chicago

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (ACTUAL)

September 1, 2017

Primary Completion (ANTICIPATED)

October 30, 2018

Study Completion (ANTICIPATED)

December 31, 2018

Study Registration Dates

First Submitted

November 6, 2017

First Submitted That Met QC Criteria

November 6, 2017

First Posted (ACTUAL)

November 8, 2017

Study Record Updates

Last Update Posted (ACTUAL)

November 13, 2017

Last Update Submitted That Met QC Criteria

November 8, 2017

Last Verified

November 1, 2017

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • CBTRA-02

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

UNDECIDED

IPD Plan Description

The investigators of this study would like to share IPD. However other cooperative institution's consent will be needed for sharing IPD.

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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