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

gc: percent gc of the bin

map: average mappability of the bin

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.