Research Projects Underway
- Identification and clinical testing of methylated DNA biomarkers for the detection of ctDNA in plasma: Early diagnosis and monitoring for cancer progression/response to treatment.
- Identification of unusual causes for cancer predisposition in high-risk groups—typically in patients/families who received negative/uninformative/limited Clinical Laboratory Improvement Amendments-approved genetic test results, to detect cryptic germline mutations, structural variants (SVs), epimutation and variance of unknown significance reclassification.
- Study modes of intergenerational inheritance/erasure of altered constitutional epigenetic states (e.g., MLH1 epimutation), which can be Mendelian and non-Mendelian. Mechanistic basis of MLH1 epimutation: Currently using Chromium (10X Genomics Chromiun technology) linked-read whole genome sequencing to identify cis/trans single nucleotide variations, SVs and retroelement mobilization as potential underlying mechanisms.
- Investigate evidence-based amendments of current universal screening algorithms for colorectal and endometrial cancer to routinely identify cases with epimutation as the cause of their mismatch repair deficiency.
Frequently Used Wet-Lab Techniques
- Whole genome bisulfite sequencing, SureSelect (deep MethylSeq), targeted bisulfite sequencing (next-generation sequencing or clonal), ChIP, promoter reporter assays, reverse-transcription polymerase chain reaction (PCR).
- Targeted pyrosequencing (detection and quantification of hot-spot mutations, CpG methylation, allelic expression, copy number variation, loss of heterozygosity). Applications: Verification, molecular diagnostics, particularly robust for formalin-fixed paraffin-embedded tissue samples.
- Development of sensitive methylation-specific real-time PCR assays (qMSP, MethyLight, MethylHeavy) to detect low-levels of DNA methylation biomarkers. Applications: Detection of ctDNA in plasma, epigenetic mosaicism.