Clonal decomposition and DNA replication states defined by scaled single cell genome sequencing

OV2295 Tables

ov2295_breakpoint_counts.csv.gz: Table of breakpoint counts per cell

• prediction_id: identifier for the breakpoint
• cell_id: identifier for the cell
• read_count: number of reads
• library_id: identifier for the DNA library
• sample_id: identifier for the sequenced sample
• chromosome_1: chromosome of breakend 1
• strand_1: orientation of break end 1
• position_1: position of break end 1
• chromosome_2: chromosome of breakend 2
• strand_2: orientation of break end 2
• position_2: position of break end 2

ov2295_cell_cn.csv.gz: Table of cell specific copy number

• cell_id: identifier for the cell
• sample_id: identifier for the sequenced sample
• library_id: identifier for the DNA library
• chr: chromosome of bin
• start: start of bin
• end: end of bin
• reads: number of reads
• copy: raw normalized copy number
• state: copy number state

ov2295_cell_metrics.csv.gz: Table of cell metrics

• cell_id: identifier of the cell
• unpaired_mapped_reads: number of unpaired mapped reads
• paired_mapped_reads: number of mapped reads that were properly paired
• unpaired_duplicate_reads: number of unpaired duplicated reads
• paired_duplicate_reads: number of paired reads that were also marked as duplicate
• unmapped_reads: number of unmapped reads
• percent_duplicate_reads: percentage of duplicate reads
• estimated_library_size: scaled total number of mapped reads
• total_reads: total number of reads, regardless of mapping status
• total_mapped_reads: total number of mapped reads
• total_duplicate_reads: number of duplicate reads
• total_properly_paired: number of properly paired reads
• coverage_breadth: percentage of genome covered by some read
• coverage_depth: average reads per nucleotide position in the genome
• median_insert_size: median insert size between paired reads
• mean_insert_size: mean insert size between paired reads
• standard_deviation_insert_size: standard deviation of the insert size between paired reads
• index_sequence: index sequence of the adaptor sequence
• column: column of the cell on the nanowell chip
• img_col: column of the cell from the perspective of the microscope
• index_i5: id of the i5 index adapter sequence
• sample_type: type of the sample
• primer_i7: id of the i5 index primer sequence
• experimental_condition: experimental treatment of the cell, includes controls
• index_i7: id of the i7 index adapter sequence
• cell_call: living/dead classification of the cell based on staining usually, C1 == living, C2 == dead
• sample_id: name of the sample
• primer_i5: id of the i5 index primer sequence
• row: row of the cell on the nanowell chip
• library_id: identifier for the DNA library
• index: ignored
• multiplier: during parameter searching, the set [1..6] that was chosen
• MSRSI_non_integerness: median of segment residuals from segment integer copy number states
• MBRSI_dispersion_non_integerness: median of bin residuals from segment integer copy number states
• MBRSM_dispersion: median of bin residuals from segment median copy number values
• autocorrelation_hmmcopy: hmmcopy copy autocorrelation
• cv_hmmcopy: ignored
• empty_bins_hmmcopy: number of empty bins in hmmcopy
• mad_hmmcopy: median absolute deviation of hmmcopy copy
• mean_hmmcopy_reads_per_bin: mean reads per hmmcopy bin
• median_hmmcopy_reads_per_bin: median reads per hmmcopy bin
• std_hmmcopy_reads_per_bin: standard deviation value of reads in hmmcopy bins
• total_halfiness: summed halfiness penality score of the cell
• total_mapped_reads_hmmcopy: total mapped reads in all hmmcopy bins
• scaled_halfiness: summed scaled halfiness penalty score of the cell
• mean_state_mads: mean value for all median absolute deviation scores for each state
• mean_state_vars: variance value for all median absolute deviation scores for each state
• mad_neutral_state: median absolute deviation score of the neutral 2 copy state
• breakpoints: number of breakpoints, as indicated by state changes not at the ends of chromosomes
• mean_copy: mean hmmcopy copy value
• state_mode: the most commonly occuring state
• log_likelihood: hmmcopy log likelihood for the cell
• true_multiplier: the exact decimal value used to scale the copy number for segmentation
• order: order of the cell in the hierarchical clustering tree
• quality: random forest classifier proability score that cell is good

ov2295_clone_alleles.csv.gz: Table of clone specific allele data

• chr: chromosome of bin
• start: start of bin
• end: end of bin
• hap_label: haplotype block identifier
• clone_id: clone identifier
• allele_1_sum: number of reads for allele 1 of the haplotype block
• allele_2_sum: number of reads for allele 2 of the haplotype block
• total_counts_sum: total reads for the haplotype block

ov2295_clone_breakpoints.csv.gz: Table of breakpoints per clone for OV2295 samples. Columns:

• prediction_id: identifier for the breakpoint
• chromosome_1: chromosome of breakend 1
• strand_1: orientation of break end 1
• position_1: position of break end 1
• chromosome_2: chromosome of breakend 2
• strand_2: orientation of break end 2
• position_2: position of break end 2
• clone_id: clone identifier
• read_count: number of reads
• is_present: presence=1, absent=0

ov2295_clone_clusters.csv.gz: Table of cell clusters as putative clones

• cell_id: identifier for the cell
• clone_id: clone identifier

ov2295_clone_cn.csv.gz: Table of allele specific copy number per clone for OV2295 samples. Columns:

• chr: chromosome of bin
• start: start of bin
• end: end of bin
• total_cn: HMMCopy predicted total copy number 
• minor_cn: HMM predicted minor copy number 
• major_cn: HMM predicted major copy number 
• clone_id: clone identifier

ov2295_clone_snvs.csv.gz: Table of SNVs per clone for OV2295 samples.  Columns:

• chrom: chromosome
• coord: genome position
• ref: reference nucleotide
• alt: alternate nucleotide
• clone_id: clone identifier
• ref_counts: number of reads at this position matching the reference nucleotide
• alt_counts: number of reads at this position matching the alternate nucleotide
• total_counts: total number of reads at this position
• is_present: presence=0, absent=1
• is_het: is heterozygous
• is_hom: is homozygous for the alternate

ov2295_nodes.csv.gz: Table of phylogenetic information for SNV evolution

• variant_id: identifier for the SNV as chrom:coord:ref:alt
• node: node in the phylogenetic tree
• loss: probability the SNV was lost at this node
• origin: probability the SNV originated at this node
• presence: probability the SNV is present at this node
• ml_origin: binary indicator the SNV originated at this node
• ml_presence: binary indicator the SNV is present at this node
• ml_loss: binary indicator the SNV was lost at this node

ov2295_snv_counts.csv.gz: Table of SNV counts

• chrom: chromosome
• coord: genome position
• ref: reference nucleotide
• alt: alternate nucleotide
• ref_counts: number of reads at this position matching the reference nucleotide
• alt_counts: number of reads at this position matching the alternate nucleotide
• cell_id: identifier for the cell
• total_counts: total number of reads at this position
• sample_id: identifier for the sequenced sample

ov2295_tree.pickle: Phylogenetic tree in python pickle format.  Requires installation of the stochastic dollo code at: https://bitbucket.org/dranew/dollo, version 0.4.2.

Note the following sample mapping: ‘SA922’: ‘OV2295(R2)’, ‘SA921’: ‘TOV2295(R)’, ‘SA1090’: ‘OV2295’,

Plots

ov_supp_clone_allele_cn.png: Clone allele ratios for each OV2295 sample.

ov_supp_clone_total_cn.png: Clone copy number for each OV2295 sample.

ov_supp_sample_total_cn.png: Bulk copy number for each OV2295 sample.

ov_supp_sample_allele_cn.png: Bulk allele ratios for each OV2295 sample.