Dna Copy Number Profiling From Bulk Tissue To Single Cells
summary
Alleloscope is an allele-specific copy number pipeline that combines pooled segmentation and EM-based phasing to call haplotype-resolved CNAs from sparse scDNA-seq and scATAC-seq. Applied to gastric, colorectal and breast tumors it reveals multi-allelic mirrored CNAs at surprising prevalence (many rare subclones per tumor), detects copy-neutral loss-of-heterozygosity, and shows concordance with linked-read validation. The method works on low-coverage single-cell profiles and links allele-specific CNAs to chromatin accessibility.
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chapters (16)
- 0:00Intro
- 3:40What is Encode
- 5:37Pilot Phase
- 7:13Genome Browser
- 8:42Random Reshuffling
- 11:15Nonparametric Approach
- 13:33Genomics After 15 Years
- 15:29Why Study Cancer
- 21:44Allele Specific Method
- 26:22Structure of Data
- 28:20Model
- 30:27Method
- 30:55Results
- 35:31Spatial Transcriptome
- 37:47Lessons Learned
- 39:58QuestionsComments
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