Name | Date modified | File size |
|
|---|---|---|---|
Concept Sheet Template | Mar 2 | — | |
[inactive] SV Analysis FG: Uddin - Multi-Tissue Landscape of Mosaic Chromosomal Alterations (mCA) Across SMaHT Donors Shared | Jul 1 | 31 KB | |
A02. Concept Sheet Summary Table Shared | Jul 7 | 19 KB | |
Benchmarking WG: Fazzio - varCUT&Tag Shared | May 26 | 198 KB | |
Benchmarking WG: Macias-Velasco (Ting Wang)-Pangenome Somatic Variant Calling Paper WashU-VAI.docx Shared | May 26 | 39 KB | |
Benchmarking WG: Niklas (Peter Park) - Characterizing Chromosome-Specific Telomere Length Using Long-Read Sequencing Shared | May 26 | 31 KB | |
Benchmarking WG: Sohn - Somatic variant discovery leveraging T2T DSA Shared | Apr 7 | 6 KB | |
Benchmarking WG: Vollger - Haplotype resolved map of somatic epimutations - Benchmarking Shared | May 26 | 32 KB | |
Benchmarking WG: benchmark_in_fibroblasts Shared | May 26 | 5 KB | |
Benchmarking WG: Kong - A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures Shared | Apr 7 | 34 KB | |
Benchmarking WG: McGee - Short- and Long-read platform benchmarking Shared | May 26 | 32 KB | |
Benchmarking WG: Sedlazeck - Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions Shared | Apr 7 | 5 KB | |
Benchmarking WG: SMaHT benchmark design Shared | May 26 | 6 KB | |
Benchmarking WG: Zhang - Benchmarking of duplex sequencing approaches to uncover somatic mutation landscapes Shared | Apr 7 | 5 KB | |
Duplex FG: Niu, Muchun - Whole Genome Scanning of Deep Variants by CompDuplex-seq Shared | May 26 | 32 KB | |
ELSI WG: Dr. Raquel Hernandez_Lessons Learned in Communicating with SMaHT Donor Families through Digital Platforms.docx Shared | Apr 3 | 38 KB | |
Functional FG: Nakao - Single-cell characterization of telomere length variation and its relationship with somatic mutations and gene expression Limited Access | Apr 3 | 33 KB | |
Functional FG: Palmer - Benchmarking Methods and Pipelines for Expressed Variant Detection with Single-Cell RNA Sequencing in the SMaHT Consortium.docx Shared | May 26 | 25 KB | |
Functional FG: Stergachis - Identifying cell-type origin of testes reads using Fiber-seq Shared | May 26 | 31 KB | |
Functional FG: 5mC and 5hmC DNA methylation landscape and their mosaisms status across human tissues (Yilei Fu) Shared | Mar 31 | 31 KB | |
Functional FG: Cell-type deconvolution from bulk functional data measurements (collaborative effort with methylation and accessibility and bulk RNAseq) Shared | Mar 31 | 30 KB | |
Functional FG: Haplotype-specific function Shared | Mar 31 | 30 KB | |
Functional FG: Minimal Viable Product (MVP) Shared | Mar 31 | 31 KB | |
Functional FG: Quantitative trait mapping using SMaHT data (will begin after first 25 donors) Shared | Mar 31 | 30 KB | |
Functional FG: Single-cell ATAC/RNA-based variant discovery Shared | Mar 31 | 30 KB | |
Functional FG: somATAC SMaHT Concept Sheet (Walsh lab TTD) Shared | Apr 3 | 32 KB | |
Functional FG: Somatic genetic and epigenetic variation within centromeres (collab. with Assembly WG) Shared | Mar 31 | 30 KB | |
Functional FG: Somatic genetic and epigenetic variation within rDNA arrays (collab. with Assembly WG) Shared | Mar 31 | 30 KB | |
Functional FG: Somatic genetic and epigenetic variation within segmental duplications (collab. with Assembly WG) Shared | Mar 31 | 30 KB | |
Functional FG: Somatic Transcriptome Shared | Mar 31 | 30 KB | |
Functional WG — Personal genomes modulate somatic evolution through cell-state landscapes Shared | Apr 27 | 197 KB | |
Genome Analysis WG: Using Donor-Specific Assemblies to Identify Reference-Induced Distortions in Read Handling Shared | May 7 | 31 KB | |
Genome Assembly FG: Assembly Focus Group: DSA-based somatic variant identification Shared | Apr 3 | 31 KB | |
Genome Assembly FG: Mack- Using a donor-specific assembly to detect somatic structural variation in COLO929 Shared | Apr 3 | 32 KB | |
Genome Assembly FG: Towards a Comprehensive Donor-Specific Assembly: Integrating Multi-Tissue Data for Accurate Representation - Park.docx Shared | Apr 3 | 13 KB | |
Genome Assembly FG: Best practices for tissue-only Genome assembly Shared | Apr 3 | 30 KB | |
Genome Assembly FG: Graph-Based Approaches for Cross-Tissue Somatic Variant Detection in Challenging Regimes Shared | Jun 30 | 31 KB | |
Genome Assembly FG: Minimal Viable Product (MVP) Shared | Apr 3 | 30 KB | |
Genome Assembly FG: Noyes - DSA-based sSNV calling.docx Shared | Jul 9 | 12 KB | |
Genome Assembly FG: Telomere analysis Shared | Apr 3 | 30 KB | |
Markowski - Chromatin Context and the Retention of Somatic Variants Across Human Tissues Shared | Jun 29 | 6 KB | |
Markowski - germline call set comparison across tissues, libraries, callers Shared | Jun 30 | 5 KB | |
MEI Analysis FG - Boxun ZHAO_Shayna MALLET—PTA-HAT-seq method paper Shared | May 26 | 5 KB | |
MEI Analysis FG: A functional landscape of transposable element–derived RNA expression in human tissues Shared | Apr 4 | 32 KB | |
MEI Analysis FG: Boxun ZHAO—HAT-seq SMaHT production paper Shared | Jun 30 | 5 KB | |
MEI Analysis FG: Burn, Voshall SMaHT Concept Sheet L1-ONT Methods Paper.docx Shared | May 26 | 20 KB | |
MEI Analysis FG: Landscape of somatic retrotransposition in human tissues Shared | Apr 3 | 33 KB | |
MEI Analysis FG: Methylation of New Germline TE Insertions & Flanking Regions Shared | May 7 | 31 KB | |
MEI Analysis FG: Somatic MEI benchmarking Shared | May 26 | 33 KB | |
MEI Analysis FG: Zhou, Mills, Boyle - Nanopore Cas9-targeted sequencing enables low-frequency somatic transposable elements detection in human brains Shared | Apr 3 | 5 KB |