University of Oxford
TARGET-seq_genotyping_data.tsv (2.57 MB)

TARGET-seq+ genotyping data

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posted on 2024-06-24, 11:44 authored by Niels Asger JakobsenNiels Asger Jakobsen, Sven Turkalj, Paresh Vyas

Genotyping data for TARGET-seq+ from bone marrow samples from 9 cases with clonal hematopoiesis and 1 control sample.

For each mutation and each single cell, data are provided for the genomic DNA amplicon (".gDNA"), the mRNA/cDNA amplicon (".mRNA"; if present) and the heterozygous germline SNP ("SNP."; if present). Where multiple mutations were amplified in a single cell, data for these are shown in separate lines.

Genotypes were called separately for the genomic DNA amplicon ("genotype.gDNA"), and the mRNA/cDNA amplicon ("genotype.mRNA"). Zygosity was called for heterozygous SNPs where these were present in the amplicon.

The final column indicates the consensus cell genotype for that mutation, integrating information from gDNA, mRNA and heterozygous SNPs.

Column descriptions

Cell = Cell ID

Sample = Donor ID

Sample_type = Type of sample; CH = clonal haematopoiesis sample; WT_control = non-CH wild-type control sample; No_template_control = empty well control

Plate = Plate ID

mutation = mutation amplified

coverage.gDNA = total coverage of locus in gDNA amplicon

Ref.gDNA = reference allele count in gDNA amplicon

Mut.gDNA = mutant allele count in gDNA amplicon

VAF.gDNA = variant allele frequency in gDNA amplicon

genotype.gDNA = genotype called in gDNA amplicon

coverage.mRNA = total coverage of locus in mRNA amplicon

Ref.mRNA = reference allele count in mRNA amplicon

Mut.mRNA = mutant allele count in mRNA amplicon

VAF.mRNA = variant allele frequency in mRNA amplicon

genotype.mRNA = genotype called in mRNA amplicon

SNP = Name of the germline SNP (if present) found near the mutation locus, covered by the gDNA amplicon

SNP.coverage = total coverage across the SNP in the gDNA amplicon

SNP.ref = reference allele count for the SNP

SNP.alt = alternate allele count for the SNP

SNP.VAF = variant allele frequency for the SNP (alternate allele)

SNP.genotype = genotype called for the SNP; Het = Heterozygous biallelic detection; Hom_Ref = homozygous reference; Hom_Alt = homozygous alternate

genotype = consensus genotype


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