Use Cases to Consider in Specimen CMET - from CG ClinSeq.doc
Use Cases to Consider in the project “Specimen CMET Second Release” Date: March 1, 2012
Clinical Genomics Workgroup’s Clinical Sequencing project (# 841) has identified several use cases which should be supported within the Specimen CMET and DAM. For more information contact Mollie Ullman-Cullere (mullmancullere@partners.org) or Daryl Thomas (Daryl.Thomas@lifetech.com) or Lynn Bry (LBry@partners.org)
Use Cases requiring explicate identification of 1 or more specimens to be used in laboratory analysis. This likely requires the identification of specimen groups (i.e. separate specimens and associated derivatives) originating from the same patient/subject or related patients/subjects.
- 1. Germline testing for biomarkers/mutations (usually inherited)
- 2. Tumor testing for somatic (tumor specific biomarkers/muations)
- a. Matched specimens for germline and somatic analysis, where comparison will result in the identification of tumor specific mutations/biomarkers
- b. Tumor specimen without a matched germline specimen, where mutations/biomarkers are believed to be specific to tumors.
- 3. Pediatric testing for biomarkers/mutations causal to rare early childhood conditions
- a. Matched specimens of patient and maternal and paternal specimens, where comparison aids in identification of original biomarkers/mutations within the patient
- 4. Prenatal testing which may be reported on the maternal medical record (and should be identified as separate from germline testing
- a. Often have matched fetal and maternal specimens for analysis
- 5. Infectious disease testing, where the biomarker/mutation identified within the disease causing organism is reported into the patient medical record following similar data standards as used for other testing scenarios above.
- 6. Microbiome analysis of a the patient
- a. Includes analysis of microorganisms living in the patients gastrointestinal tract or Genitourinary system
Derivatives which may be analyzed from the above testing scenarios include: DNA, RNA, and Protein
