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

<p><strong>OV2295&nbsp;Tables</strong></p> <p>ov2295_breakpoint_counts.csv.gz: Table of breakpoint counts per cell</p> <ul> <li>prediction_id: identifier for the breakpoint</li> <li>cell_id: identifier for the cell</li> <li>read_count: number of reads</li> <li>library_id: identifier for the DNA library</li> <li>sample_id: identifier for the sequenced sample</li> <li>chromosome_1: chromosome of breakend 1</li> <li>strand_1: orientation of break end 1</li> <li>position_1: position of break end 1</li> <li>chromosome_2: chromosome of breakend 2</li> <li>strand_2: orientation of break end 2</li> <li>position_2: position of break end 2</li> </ul> <p>ov2295_cell_cn.csv.gz: Table of cell specific copy number</p> <ul> <li>cell_id: identifier for the cell</li> <li>sample_id: identifier for the sequenced sample</li> <li>library_id: identifier for the DNA library</li> <li>chr: chromosome of bin</li> <li>start: start of bin</li> <li>end: end of bin</li> <li>reads: number of reads</li> <li>copy: raw normalized copy number</li> <li>state: copy number state</li> <li>gc: percent gc of the bin</li> <li>map: average mappability of the bin</li> </ul> <p>ov2295_cell_metrics.csv.gz: Table of cell metrics</p> <ul> <li>cell_id: identifier of the cell</li> <li>unpaired_mapped_reads: number of unpaired mapped reads</li> <li>paired_mapped_reads: number of mapped reads that were properly paired</li> <li>unpaired_duplicate_reads: number of unpaired duplicated reads</li> <li>paired_duplicate_reads: number of paired reads that were also marked as duplicate</li> <li>unmapped_reads: number of unmapped reads</li> <li>percent_duplicate_reads: percentage of duplicate reads</li> <li>estimated_library_size: scaled total number of mapped reads</li> <li>total_reads: total number of reads, regardless of mapping status</li> <li>total_mapped_reads: total number of mapped reads</li> <li>total_duplicate_reads: number of duplicate reads</li> <li>total_properly_paired: number of properly paired reads</li> <li>coverage_breadth: percentage of genome covered by some read</li> <li>coverage_depth: average reads per nucleotide position in the genome</li> <li>median_insert_size: median insert size between paired reads</li> <li>mean_insert_size: mean insert size between paired reads</li> <li>standard_deviation_insert_size: standard deviation of the insert size between paired reads</li> <li>index_sequence: index sequence of the adaptor sequence</li> <li>column: column of the cell on the nanowell chip</li> <li>img_col: column of the cell from the perspective of the microscope</li> <li>index_i5: id of the i5 index adapter sequence</li> <li>sample_type: type of the sample</li> <li>primer_i7: id of the i5 index primer sequence</li> <li>experimental_condition: experimental treatment of the cell, includes controls</li> <li>index_i7: id of the i7 index adapter sequence</li> <li>cell_call: living/dead classification of the cell based on staining usually, C1 == living, C2 == dead</li> <li>sample_id: name of the sample</li> <li>primer_i5: id of the i5 index primer sequence</li> <li>row: row of the cell on the nanowell chip</li> <li>library_id: identifier for the DNA library</li> <li>index: ignored</li> <li>multiplier: during parameter searching, the set [1..6] that was chosen</li> <li>MSRSI_non_integerness: median of segment residuals from segment integer copy number states</li> <li>MBRSI_dispersion_non_integerness: median of bin residuals from segment integer copy number states</li> <li>MBRSM_dispersion: median of bin residuals from segment median copy number values</li> <li>autocorrelation_hmmcopy: hmmcopy copy autocorrelation</li> <li>cv_hmmcopy: ignored</li> <li>empty_bins_hmmcopy: number of empty bins in hmmcopy</li> <li>mad_hmmcopy: median absolute deviation of hmmcopy copy</li> <li>mean_hmmcopy_reads_per_bin: mean reads per hmmcopy bin</li> <li>median_hmmcopy_reads_per_bin: median reads per hmmcopy bin</li> <li>std_hmmcopy_reads_per_bin: standard deviation value of reads in hmmcopy bins</li> <li>total_halfiness: summed halfiness penality score of the cell</li> <li>total_mapped_reads_hmmcopy: total mapped reads in all hmmcopy bins</li> <li>scaled_halfiness: summed scaled halfiness penalty score of the cell</li> <li>mean_state_mads: mean value for all median absolute deviation scores for each state</li> <li>mean_state_vars: variance value for all median absolute deviation scores for each state</li> <li>mad_neutral_state: median absolute deviation score of the neutral 2 copy state</li> <li>breakpoints: number of breakpoints, as indicated by state changes not at the ends of chromosomes</li> <li>mean_copy: mean hmmcopy copy value</li> <li>state_mode: the most commonly occuring state</li> <li>log_likelihood: hmmcopy log likelihood for the cell</li> <li>true_multiplier: the exact decimal value used to scale the copy number for segmentation</li> <li>order: order of the cell in the hierarchical clustering tree</li> <li>quality: random forest classifier proability score that cell is good</li> </ul> <p>ov2295_clone_alleles.csv.gz: Table of clone specific allele data</p> <ul> <li>chr: chromosome of bin</li> <li>start: start of bin</li> <li>end: end of bin</li> <li>hap_label: haplotype block identifier</li> <li>clone_id: clone identifier</li> <li>allele_1_sum: number of reads for allele 1 of the haplotype block</li> <li>allele_2_sum: number of reads for allele 2 of the haplotype block</li> <li>total_counts_sum: total reads for the haplotype block</li> </ul> <p>ov2295_clone_breakpoints.csv.gz:&nbsp;Table of breakpoints per clone for OV2295 samples. Columns:</p> <ul> <li>prediction_id: identifier for the breakpoint</li> <li>chromosome_1: chromosome of breakend 1</li> <li>strand_1: orientation of break end 1</li> <li>position_1: position of break end 1</li> <li>chromosome_2: chromosome of breakend 2</li> <li>strand_2: orientation of break end 2</li> <li>position_2: position of break end 2</li> <li>clone_id: clone identifier</li> <li>read_count: number of reads</li> <li>is_present: presence=1, absent=0</li> </ul> <p>ov2295_clone_clusters.csv.gz: Table of cell clusters as putative clones</p> <ul> <li>cell_id: identifier for the cell</li> <li>clone_id: clone identifier</li> </ul> <p>ov2295_clone_cn.csv.gz:&nbsp;Table of allele specific copy number per clone for OV2295 samples. Columns:</p> <ul> <li>chr: chromosome of bin</li> <li>start: start of bin</li> <li>end: end of bin</li> <li>total_cn: HMMCopy predicted total copy number&nbsp;</li> <li>minor_cn: HMM predicted minor copy number&nbsp;</li> <li>major_cn: HMM predicted major copy number&nbsp;</li> <li>clone_id: clone identifier</li> </ul> <p>ov2295_clone_snvs.csv.gz:&nbsp;Table of SNVs per clone for OV2295 samples.&nbsp; Columns:</p> <ul> <li>chrom: chromosome</li> <li>coord: genome position</li> <li>ref: reference nucleotide</li> <li>alt: alternate nucleotide</li> <li>clone_id: clone identifier</li> <li>ref_counts: number of reads at this position matching the reference nucleotide</li> <li>alt_counts: number of reads at this position matching the alternate nucleotide</li> <li>total_counts: total number of reads at this position</li> <li>is_present: presence=0, absent=1</li> <li>is_het:&nbsp;is heterozygous</li> <li>is_hom: is homozygous for the alternate</li> </ul> <p>ov2295_nodes.csv.gz: Table of phylogenetic information for SNV evolution</p> <ul> <li>variant_id: identifier for the SNV as chrom:coord:ref:alt</li> <li>node: node in the phylogenetic tree</li> <li>loss: probability the SNV was lost at this node</li> <li>origin: probability the SNV originated at this node</li> <li>presence: probability the SNV is present at this node</li> <li>ml_origin: binary indicator the SNV originated at this node</li> <li>ml_presence: binary indicator the SNV is present at this node</li> <li>ml_loss: binary indicator the SNV was lost at this node</li> </ul> <p>ov2295_snv_counts.csv.gz: Table of SNV counts</p> <ul> <li>chrom: chromosome</li> <li>coord: genome position</li> <li>ref: reference nucleotide</li> <li>alt: alternate nucleotide</li> <li>ref_counts: number of reads at this position matching the reference nucleotide</li> <li>alt_counts: number of reads at this position matching the alternate nucleotide</li> <li>cell_id: identifier for the cell</li> <li>total_counts: total number of reads at this position</li> <li>sample_id: identifier for the sequenced sample</li> </ul> <p>ov2295_tree.pickle: Phylogenetic tree in python pickle format.&nbsp; Requires installation of the stochastic dollo code at: https://bitbucket.org/dranew/dollo, version 0.4.2.</p> <p>Note the following sample mapping: &lsquo;SA922&rsquo;: &lsquo;OV2295(R2)&rsquo;, &lsquo;SA921&rsquo;: &lsquo;TOV2295(R)&rsquo;, &lsquo;SA1090&rsquo;: &lsquo;OV2295&rsquo;,</p> <p><strong>Plots</strong></p> <p>ov_supp_clone_allele_cn.png: Clone allele ratios for each OV2295 sample.</p> <p>ov_supp_clone_total_cn.png: Clone copy number for each OV2295 sample.</p> <p>ov_supp_sample_total_cn.png: Bulk copy number for each OV2295 sample.</p> <p>ov_supp_sample_allele_cn.png: Bulk allele ratios for each OV2295 sample.</p>