PURPLE is a purity ploidy estimator primarily designed for whole genome sequenced (WGS) data. It combines B-allele frequency (BAF) from AMBER, read depth ratios from COBALT, somatic variants and structural variants to estimate the purity and copy number profile of a tumor sample. PURPLE supports both grch 37 and 38 reference assemblies.
PURPLE may also be run on targeted data. For more info please see here
- Installation
- Arguments
- Input
- Tumor Only Mode
- Germline Only Mode
- Algorithm
- 1. Sex
- 2. Segmentation
- 3. Sample Purity and Ploidy
- 4. Copy Number Smoothing
- 5. Inferring copy number for regions without read depth information
- 6. Allele specific copy number inferring
- 7. Structural Variant Recovery
- 8. Identify germline gene_deletions
- 9. Determine a QC Status for the tumor
- 10. Somatic enrichment
- 11. Germline enrichment
- 12. Driver Identification
- Output
- Version History / Download Links
To install, download the latest compiled jar file from the download links. PURPLE also requires the same GC profile as used in COBALT (available from HMFTools-Resources > DNA Pipeline and a reference genome. While these are sufficient to run PURPLE there are a number of optional dependencies that provide additional functionality.
To generate output charts, PURPLE depends on a number of bioconductor packages. After installing R or RStudio, the chart dependencies can be installed with the following R commands:
library(BiocManager)
install("VariantAnnotation")
install("dplyr")
install("ggplot2")
Alternatively, PURPLE can be run with the no_charts argument which will eliminate the R dependency.
To generate the CIRCOS output, CIRCOS must be downloaded and installed.
Unlike the charts above, CIRCOS charts are not generated by default but only if the circos argument is provided.
To populate a database with the PURPLE output, please follow the instructions in the database section.
PURPLE requires Java 11+ and can be run with the minimum set of arguments as follows:
java -jar purple.jar \
-reference COLO829R \
-tumor COLO829T \
-amber /path/COLO829/amber \
-cobalt /path/COLO829/cobalt \
-gc_profile /path/GC_profile.1000bp.37.cnp \
-ref_genome_version 37 \
-ref_genome /path/Homo_sapiens_assembly37.fasta \
-ensembl_data_dir /path_to_ensembl_data_cache/ \
-output_dir /output/purple/ \
Purple requires a GRIDSS + Gripss VCF for structural variants, and Sage for somatic variants.
java -jar purple.jar \
-reference COLO829R \
-tumor COLO829T \
-amber /path/COLO829/amber \
-cobalt /path/COLO829/cobalt \
-gc_profile /path/GC_profile.1000bp.37.cnp \
-ref_genome /path/Homo_sapiens_assembly37.fasta \
-ref_genome_version 37 \
-ensembl_data_dir /path_to_ensembl_data_cache/ \
-somatic_vcf /path/COLO829/COLO829.somatic.vcf.gz \
-somatic_sv_vcf /path/COLO829/COLO829.sv.vcf.gz \
-sv_recovery_vcf /path/COLO829/COLO829.sv.low_confidence.vcf.gz \
-circos /path/circos-0.69-6/bin/circos \
-output_dir /output/purple/ \
| Argument | Description |
|---|---|
| reference | Name of the reference sample. This should correspond to the value used in AMBER and COBALT. |
| tumor | Name of the tumor sample. This should correspond to the value used in AMBER and COBALT. |
| output_dir | Path to the output directory. This directory will be created if it does not already exist. |
| amber | Path to AMBER output. This should correspond to the output_dir used in AMBER. |
| cobalt | Path to COBALT output. This should correspond to the output_dir used in COBALT. |
| gc_profile | Path to GC profile. |
| ref_genome | Path to reference genome fasta file. |
| ref_genome_version | 37 (default) or 38 |
| ensembl_data_dir | Path to Ensembl data cache |
The GC Profile file used by HMF (GC_profile.1000bp.37.cnp) is available to download from HMFTools-Resources > DNA Resources. A 38 equivalent is also available.
| Argument | Default | Description |
|---|---|---|
| threads | 2 | Number of threads to use for ploidy & purity fitting routine |
| germline_vcf | None | Optional location of germline variants VCF. Sample names must match reference parameter. GZ files supported. |
| somatic_vcf | None | Optional location of somatic variants vcf |
| somatic_sv_vcf | None | Optional location of somatic structural variants VCF for fitting and annotation |
| germline_sv_vcf | None | Optional location of germline structural variants variants VCF for annotation |
| sv_recovery_vcf | None | Optional location of low confidence structural variants VCF which may be recovered by Purple |
| germline_del_freq_file | None | Provide a cohort frequency for germline deletions |
| circos | None | Optional path to circos binary. When supplied, circos graphs will be written to <output_dir>/plot |
| no_charts | NA | Disables creation of (non-circos) charts |
The following arguments control the somatic fit. Changing these values without a thorough understanding of the system is not recommended.
| Argument | Default | Description |
|---|---|---|
| somatic_min_peak | 10 | Minimum number of somatic variants to consider a peak. |
| somatic_min_variants | 10 | Minimum number of somatic variants required to assist highly diploid fits. |
| somatic_min_purity | 0.17 | Somatic fit will not be used if both somatic and fitted purities are less than this value. |
| somatic_min_purity_spread | 0.15 | Minimum spread within candidate purities before somatics can be used. |
| somatic_penalty_weight | 1 | Proportion of somatic penalty to include in fitted purity score. |
| highly_diploid_percentage | 0.97 | Proportion of genome that must be diploid before using somatic fit. |
The following arguments control the smoothing process. Changing these values without a thorough understanding of the system is not recommended.
| Argument | Default | Description |
|---|---|---|
| min_diploid_tumor_ratio_count | 30 | Always smooth over contiguous segments which are fewer than this number of depth windows long and which have no SV support on either side and which are bounded on both sides by copy number regions which could be smoothed together using our normal smoothing rules. This is intended to assist with smoothing residual GC noise in regions of very high or low GC content. This parameter only works when a SV vcf is provided. |
| min_diploid_tumor_ratio_count_centromere | 150 | Always smooth over copy number breakpoints which are fewer than this number of depth windows from the centromere or telomere and which have no further SV breakpoints nearer to the the centromere or telomere. This is intended to help smooth over noisy mapping in repetitive regions close to the telomere and centromere. |
The following arguments control the fitting behaviour. Changing these values without a thorough understanding of the system is not recommended.
| Argument | Default | Description |
|---|---|---|
| min_ploidy | 1 | Minimum ploidy to fit |
| max_ploidy | 8 | Maximum ploidy to fit |
| min_purity | 0.08 | Minimum purity to fit to |
| max_purity | 1 | Maximum purity to fit to |
| purity_increment | 0.01 | Sets the increment from min to max purity |
Min/max purity/ploidy arguments are inclusive.
Purity increments at a fixed rate. Ploidy, however, increments according to the following schedule:
| Min Ploidy | Max Ploidy | Increment |
|---|---|---|
| 0 | 3 | 0.02 |
| 3 | 5 | 0.05 |
| 5 | 5+ | 0.1 |
The following arguments control the driver catalog behaviour.
| Argument | Description |
|---|---|
| somatic_hotspots | VCF of somatic hotspot locations. Mandatory if driver catalog enabled. |
| germline_hotspots | VCF of germline hotspot locations. Mandatory if driver catalog enabled and germline variants supplied. |
| driver_gene_panel | TSV of driver genes, enables search for drivers and writing of driver catalog files |
The hotspot VCF used by HMF (KnownHotspots.37.vcf.gz) is available to download from HMFTools-Resources > DNA Resources. A 38 equivalent is also available. The file is used to re-annotate all somatic variants with a HOTSPOT or NEAR_HOTSPOT flag if they are on or within 5 bases of a hotspot. Hotspots are assigned a driver likelihood of 1.
The driver gene panel (DriverGenePanel.37.tsv) and 38 equivalent is also available from HMFTools-Resources > DNA Resources
Note that generating the driver catalog for SNVs assumes that the VCF has been annotated with PAVE.
The PURPLE algorithm relies on the BAF and read depth ratio output from AMBER and COBALT respectively. They should both be run before running PURPLE.
It is also strongly recommended to run PURPLE with a high quality set of somatic SNV and INDEL calls and somatic structural variant calls.
COBALT determines the read depth ratios of the supplied tumor and reference genomes.
COBALT starts with the raw read counts per 1,000 base window for both normal and tumor samples by counting the number of alignment starts in the respective bam files with a mapping quality score of at least 10 that is neither unmapped, duplicated, secondary, nor supplementary. Windows with a GC content less than 0.2 or greater than 0.6 or with an average mappability below 0.85 are excluded from further analysis.
Next we apply a GC normalization to calculate the read ratios. We divide the read count of each window by the median read count of all windows sharing the same GC content then normalise further to the ratio of the median to mean read count of all windows.
Finally, the reference sample ratios have a further ‘diploid’ normalization applied to them to remove megabase scale GC biases. This normalization assumes that the median ratio of each 10Mb window (minimum 1Mb readable) should be diploid for autosomes and haploid for sex chromosomes in males in the germline sample.
For more information on how to run COBALT please refer to the readme.
AMBER calculates the BAF of the tumor sample by finding heterozygous locations in the reference sample from a panel of 1,344,880 common germline heterozygous SNP loci. The loci were chosen by running the GATK HaplotypeCaller over 1700 germline samples and then selecting all SNP sites which are heterozygous in 800 to 900 of the samples.
To ensure that we only capture heterozygous points, we filter the panel to only loci with allelic frequencies in the reference sample between 40% and 65% and with depth between 50% and 150% of the reference sample genome wide average. Furthermore, we filter any loci with a mapping quality < 1 or base quality < 13. This typically yields 500k-540k heterozygous germline variants per patient.
As part of a contamination check, AMBER also finds sites in the tumor that are homozygous in the reference sample using the same panel as above. A sample is considered contaminated if at least 2000 of these sites contain 3 or more reads supporting an alt in the tumor. In this case we model the expected number of non-homozygous sites using a poisson distribution and estimate a contamination percent. The result of this is included in the amber QC output file.
For more information on how to run AMBER please refer to the readme.
Providing a high quality set of somatic structural variant calls to PURPLE allows exact base resolution of copy number changes. An accurate estimation of VAF at each breakend also allows PURPLE to infer copy number changes even across very short segments of the genome where a depth based estimation is inaccurate or impractical. Finally, PURPLE also supports recovery of filtered structural variant calls
A VCF with germline structural variants can also be provided. PURPLE can annotate such variants with purity adjusted local and variant copy number estimations in the tumor. Also, this information can be used to make calling of germline deletions more accurate.
For these purposes, PURPLE provides full support and integration with the structural variant caller GRIDSS. GRIDSS can be run directly on tumor and reference BAMs. Alternatively a lightweight version of GRIDSS can be used to re-analyse a set of variant calls and provide additional filtering and accurate VAF estimation.
A high quality set of somatic SNV and INDEL calls can also improve the accuracy and utility of PURPLE. If provided, passing (or unfiltered) variants enhance the purity and ploidy fit in 2 ways. Firstly, each solution receives a penalty for the proportion of somatic variants which have implied variant copy numbers that are inconsistent with the minor and major allele copy number. Secondly, for highly diploid samples, the VAFs of the somatic variants are used directly to calculate a somatic variant implied purity.
For both purposes, accurate VAF estimation is essential thus PURPLE requires the ‘AD’ (Allelic Depth) and 'DP' (Depth) fields in the vcf. High quality filtering of artifacts and false positive calls is also critical to achieving an accurate fit. SAGE is the recommended input somatic variant caller.
If a similar VCF of germline SNV and INDEL variants is provided, PURPLE will annotate them with additional fields described here.
Whilst PURPLE is primarily designed to be run with paired normal / tumor data, it is possible to run with tumor data only by leaving the reference and reference_bam parameters null. It is important to first run AMBER and COBALT in tumor only mode.
AMBER and COBALT have native support for tumor only as described in their respective readme files.
Tumor only mode impacts PURPLE in the following ways:
- Somatic variants are excluded from fitting
- X and Y chromosomes are excluded from fitting
- Gender is determined only from AMBER
- COBALT allosome reference ratios are adjusted according to AMBER gender
- No germline chromosomal aberrations are detected
- HLA SNV / INDEL are ignored and hard filtered (assumed to be germline)
- somatic SNV/INDEL and SV with PON_ filters are hardfiltered and ignored
Example command:
java -jar purple.jar \
-tumor COLO829T \
-amber /path/COLO829/amber \
-cobalt /path/COLO829/cobalt \
-gc_profile /path/GC_profile.1000bp.37.cnp \
-ref_genome_version 37 \
-ref_genome /path/Homo_sapiens_assembly37.fasta \
-ensembl_data_dir /path_to_ensembl_data_cache/ \
-somatic_vcf /path/COLO829/COLO829.somatic.vcf.gz \
-structural_vcf /path/COLO829/COLO829.sv.high_confidence.vcf.gz \
-sv_recovery_vcf /path/COLO829/COLO829.sv.low_confidence.vcf.gz \
-run_drivers \
-driver_gene_panel /path/DriverGenePanel.37.tsv \
-circos /path/circos-0.69-6/bin/circos \
-output_dir /output/purple/ \
Purple can be run in a limited mode on germline only output so that germline point mutations and structural variants can be annotated and filtered according to below described logic. The differences in germline mode are:
- use ONLY reference pcf from COBALT
- Amber observedBAF assumed to be 0.5 for all regions
- No somatic fit conducted. purity set to 1; ploidy to 2
- somatic VCF tags are set to fixed values PURPLE_CN: 2, PURPLE_MACN: 1, PURPLE_AF: 0.5, PURPLE_VCN: 1, BIALLELIC: FALSE
- All TMB fields are set to zero
- No geneCopyNumber,somatic or sv output is produced
- A 'somatic likelihood' is calculated (see somatic enrichment section below)
Example command:
java -jar purple.jar \
-reference COLO829R \
-amber /path/COLO829/amber \
-cobalt /path/COLO829/cobalt \
-gc_profile /path/GC_profile.1000bp.37.cnp \
-ref_genome_version 37 \
-ref_genome /path/Homo_sapiens_assembly37.fasta \
-ensembl_data_dir /path_to_ensembl_data_cache/ \
-germline_hotspots /path/KnownHotspots.germline.37.vcf.gz \
-germline_del_freq_file /path/cohort_germline_del_freq.csv \
-germline_vcf /path/COLO829/COLO829.germline.vcf.gz \
-run_drivers \
-driver_gene_panel /path/DriverGenePanel.37.tsv \
-output_dir /output/purple/ \
There are 12 key steps in the PURPLE pipeline described in detail below:
We examine both the AMBER and COBALT data to independently determine and validate the sex of the patient. This includes detecting the presence of Klinefelter syndrome: a chromosomal disorder resulting in 2 or more X chromosome in a male and which we have found to affect 0.2% of the male samples in our cohort.
To determine the sex of a sample with AMBER, we examine the number of heterozygous loci in our provided BED file of ommon germline SNPs on the X chromosome, outside the pseudoautosomal region. If the X chromosome contains < 1% of total heterozygous loci for the sample, then it is considered male.
To determine sex using COBALT, we first use the reference ratio to determine the number of copies of the X chromosome. A median X ratio greater than 0.65 is interpreted as 2 copies (note that nearly all female samples are very close to a ratio of 1, but a handful are significantly lower with mosaic X loss). If there is only one copy of the X chromosome the sample is male. Otherwise, we check for the presence of the Y chromosome as determined by at least 1000 data points with a median ratio > 0.05. If the Y chromosome is present (in addition to the 2 copies of the X chromosome), then the sample is male with Klinefelter syndrome. In the absence of the Y chromosome the sample is female.
Finally we compare the AMBER and COBALT sexes. If they are inconsistent we use the COBALT sex and flag the sample has having failed sex validation.
We segment the genome into regions of uniform copy number by combining segments generated from the COBALT read ratios for both tumor and reference sample, the BAF points from AMBER, and passing structural variant breakpoints derived from GRIPSS both germline and somatic. Read ratios and BAF points are segmented independently using the Bioconductor copynumber package which uses a piecewise constant fit (PCF) algorithm (with custom settings: gamma = 100, k =1). These segment breaks are then combined with the structural variants breaks according to the following rules:
- Every structural variant break starts a new segment, as does chromosome starts, ends and centromeres.
- Ratio and BAF segment breaks are only included if they are at least one complete mappable read depth window away from an existing segment.
If the segments identified by the PCF algorithm are not contiguous, then there remains some uncertainty about the actual start position of the segment. To address this, we use the PCF break as the start position but also include a min and max start position to capture the uncertainty. Segments with SV support are never uncertain.
Once the segments have been established we map our observations to them. In each segment we take the median BAF of the tumor sample and the median read ratio of both the tumor and reference samples. We also record the number of BAF points within the segment as the BAFCount and the number of tumor read depth windows within the segment as the depth window count.
A reference sample copy number status is determined at this stage based on the observed mean read depth ratio in the reference sample, either ‘DIPLOID’ (0.85 <= ratio <= 1.15), ‘HETEROZYGOUS_DELETION’ (0.1 <= ratio < 0.85), ‘HOMOZYGOUS_DELETION’ (ratio < 0.1), ‘AMPLIFICATION’ (1.15 < ratio <= 2.2) or ‘NOISE’ (ratio > 2.2). The 'diploid normalised' mean read depth ratio is used for this annotation. However, if a continuous region of >5MB has diploidNormalisedRatio / rawRatio < 0.7 or >1.3 (aside from the following noisy regions chr1:1-50M, chr9:135M-end, chr17:75M-end, chr19:1-20M), then this likely indicates a (rare) large copy number event the raw ratio is used instead. Regions within 2MB of a centromere and in the IG and TCR regions are further masked. The purity fitting and smoothing steps below use only the DIPLOID germline segments.
To estimate purity and sample ploidy, we use a model which considers a matrix of all possible sample purities and ploidies and scores each possible combination on a segment by segment basis, based on a set of principles which aim to choose the most parsimonious solution for the fit.
The specific scoring principles applied are the following:
- Penalise sub-clonality: The major and minor allele of each segment should be close to an integer ploidy for clonal solutions. Due to sampling noise, small deviations from integer copy numbers will be observed even, but larger deviations require subclonal features and are penalised.
- Penalise solutions which deviate from diploid heterozygous copy number: Loss of heterozygosity or loss of gain of chromosomal segments requires assumptions additional biological complexity, with the complexity increasing for larger deviations from diploid. PURPLE uses an event penalty to explicitly penalise deviations from diploid heterozygous copy number
- Penalise solutions with implausible somatic SNV copy numbers: SNVs in principle occur on only one chromatid and should not be found on both alleles. Therefore we penalise solutions where SNV copy numbers exceed the major allele copy number.
- Weigh segments by count of BAF observations: Segments are weighted by the count of BAF observations which is treated as a proxy for confidence of BAF and read depth ratio inputs.
- Place more weight on segments with higher observed BAF: segments with lower observed BAFs have more degenerate fits and are weighted less in the fit
For each [sample ploidy, purity] combination we calculate a fit score using the following formula
Fit Score = DeviationPenalty * EventPenaltyMultiplier + SomaticDeviationPenalty
The [sample ploidy, purity] combination with the lowest fit score is selected by PURPLE as the final fit score.
Each of the 3 penalty terms is described in detail in the following sections.
The deviation penalty aims to penalise [ploidy|purity] combinations which require extensive sub-clonality to explain the observed copy number pattern.
For each [ploidy|purity] combination tested an implied major and minor allele copy number is calculated based on the observed BAF and depth ratio. Purities are considerd in the range of 7% to 100% in 1% increments or 0.5% increments below 20%. A deviation penalty is then calculated for each segment for both minor and major allele based on the implied copy numbers (note Y chromosome, X chromsome for males & chromosomes with detected germline aberrations are all excluded from fitting). The function used is designed to explicitly capture a set of intuitive rules relating to known biology of cancer genomes, specifically:
- For major allele copy number > 1 and minor allele copy number > 0 a deviation penalty applies to penalise solutions which imply subclonality:
- the penalty depends only on the distance to the nearest integer copy number and varies between a minimum of a small baseline deviation [0.2] and a max of 1.
- small deviations from an integer don’t occur any additional penalty, but once a certain noise level is exceeded the penalty grows rapidly to the maximum penalty reflecting the increasing probability that the observed deviation requires an implied non-integer (subclonal) copy number.
- The deviation penalty is increased more slowly at lower purities reflecting the increased expected noise. This is implemented by modeling the penalty as a normal distribution with the standard deviation a function of the purity.
- An additional and increasing penalty multiplier applies for implied major allele copy number < 1. This is intended to capture the relative rarity of large homozygous deletions in cancer genomes, so potential solutions with significant amounts of homozygous deletion are penalised significantly.
- An additional and increasing penalty also applies for implied minor allele copy number < 0 to strongly penalise solutions which imply negative copy number and are biologically implausible.
The following chart illustrates the deviation penalty applied for each of minor and major allele copy number at both 30% and 70% purity.
The total deviation penalty is calculated by adding the minor and major allele deviation penalty. It is weighted by the observedBAF (which varies between 0.5 and 1) to reflect that higher BAF regions have fewer possible solutions. The formula used is:
Deviation Penalty = (MinorAlleleDeviationPenalty + MajorAlleleDeviationPenalty) * ObservedBAF
An event penalty is intended to further penalise [sample ploidy,purity] combinations based on the number of alterations required to get from a normal diploid chromosome to the implied minor and major allele copy number. In particular, this model penalises higher ploidy solutions that can be highly degenerate and lead to low deviation penalties, but are unlikely to be the most parsimonious or biologically plausible solution.
The event penalty multiplier is given by:
EventPenalty = 1 + 0.3 * min(SingleEventDistance, WholeGenomeDoublingDistance);
WholeGenomeDoublingDistance = 1 + abs(majorAllele - 2) + abs(minorAllele - 2);
SingleEventDistance = abs(majorAllele - 1) + abs(minorAllele - 1);
Note that a diploid segment with implied minor allele copy number = implied major allele copy number = 1 has an event penalty of exactly 1 whilst all other solutions have increasingly higher multipliers as the minor and major allele deviate further from 1. The formula includes an explicit reduced penalty for a doubling of both major and minor allele copy number since there is a known common mechanism of whole genome doubling which can occur in a single event.
The Deviation Penalty and Event Penalty are aggregated independently across all segments that are diploid in the germline and have a tumor depth ratio of <3x the average depth. An average is calculated for each value weighted by the number of BAF observations in each segment. The averaged numbers are multiplied by each other to form an overall ploidy penalty for the sample.
The following chart shows the combined shape of the deviation and event penalty:
If somatic variants are provided, an additional somatic penalty is added to fits which lead to somatic variants with variant copy number higher than the major allele copy number, since these are biologically implausible. This feature was introduced primarily to deal with a degeneracy where in certain situations a lower purity, lower ploidy solutions may provide a plausible minor and major allele copy number fit to the copy number data, but imply that many SNVs exceed the major allele copy number which is biologically implausible.
The somatic penalty is determined for each [sample ploidy,purity] combination by sampling 1000 somatic SNV per tumor and comparing the observed major allele copy number with an upper bound expectation of the variant’s copy number from the 99.9% percentile of a binomial distribution given the major allele at the SNV location. The penalty applied to a single SNV is the max(0,implied SNV copy number - 99.9% expected bound given the major allele). The somatic penalty is averaged across the 1000 variants and multiplied by a somaticPenaltyWeight [1.5] constant and added to the ploidy penalty.
While the lowest scoring purity becomes the fitted purity, we also examine other solutions within 10% or 0.0005 of the best solution. These become potential candidates if we need to resort to using the somatic purity described below. We also record the min and max of the purity, ploidy and diploid proportions of the candidates to give some context around the confidence in the solution.
Note that a segment is diploid only if both the major and minor allele are between 0.8 and 1.2 inclusive.
If any of the candidate solutions are highly diploid (>= 0.97), PURPLE checks first for the presence of TUMOR. If NONE of the following criteria are satisfied, then PURPLE sets qcStatus = FAIL_NO_TUMOR, fitMethod=NO_TUMOR and sets purity to min_purity value [0.08]:
- Tumor has one or more HOTSPOT SV or point mutation
- SNV sum(allele read count) > 1000
- SV sum(startTumorVariantFragmentSupport) > 1000 (excluding SGL breakends)
- Tumor has 3000 BAF points in germline DIPLOID regions regions with tumor ratio < 0.8 OR > 1.2 (ie. evidence of at least some aneuploidy)
If a tumor is detected, and there is a wide range (>= 0.15) of valid purities in the candidate solutions and a somatic point mutation vcf has been supplied then a somatic mode of fitting is triggered, since there may be insufficient copy number events to resolve a purity. In this case, PURPLE fits somatic peaks in VAF space.
First PURPLE groups all somatic SNV by VAF with 0.8 x AverageTumorDepth < totalReadCount < 1.2x AverageTumorDepth (after applying the following filters: !GNOMAD; TIER!=LOW_CONFIDENCE; repeatCount<4; germlineStatus='DIPLOID'; mappability=1; GermlineAlleleReadCount = 0 to ensure that all germline and other artefacts are strictly removed). A kernel density estimator is used to find peaks in the VAF range [min_purity-min(0.5,max_purity)], and the somatic fitted purity is set to 2* the highest VAF peak with weight > max(4,3% SNV count in depth range). If no peak meets this criteria but the sample has at least 10 SNV within the depth range in total choose 2 * VAF peak with the greatest count, else set the purity to min_purity [0.08]
If (somatic fitted purity and the copy number fitted purity are both < 0.17 AND the somatic purity > copy number purity) OR if there are no SNV that meet the VAF criteria OR if the somatic fit suggests biologically unlikely significant homozygous deletions (specifically more than 0.3% of depth windows have copyNumber < 0.5 excluding chrY and chr9 CDKN2A region), then use the copy number fit and set fitMethod = NORMAL. Otherwise use the somatic fitted purity, set ploidy =2 and set fit method = SOMATIC.
Finally, in case of tumors with very low SNV counts (<1000 total SNV) but with known hotspot mutations, PURPLE checks if the VAF of any hotspot mutations is not outside the expected distribution of the fitted somatic VAF peak (p<0.01). If the VAF of the hotspot is significantly higher than the fitted VAF peak, then PURPLE sets the purity to 2x maximum hotspot VAF.
Since the initial segmentation algorithm is highly sensitive, and there is a significant amount of noise in the read depth in whole genome sequencing, many adjacent segments will have a similar copy number and BAF profile and are unlikely to represent a real somatic copy number change in the tumor. We therefore apply a smoothing algorithm to merge the raw segments into a final set of smoothed copy number regions.
The following criteria apply when deciding to merge segments:
- Never merge across a segment breakpoint with structural variant support.
- Do not merge segments if the minimum BAF count in the segments being compared > 0 and the change in observed BAF > 0.03 and the minor allele tolerance is exceeded. The absolute minor allele tolerance is 0.3 + 0.5 * max(copy number of compared segments) / sqrt (min count of BAF points ). For tumors with purity < 20% the absolute tolerances are increased inversely proportional to the purity to allow for greater noise in tumor copy number and BAF measurements.
- Merge segments where the absolute or relative difference in either the copy number or ref normalised copy number is within tolerances. Absolute copy number tolerance is 0.3 + 1 / sqrt(min depth window count). Relative copy number tolerance is 0.12 + 0.8 / sqrt(min depth window count). Ref normalised copy number uses the actual germline ratios rather than the typical (1 for autosomes, 0.5 for Y etc.). Again, for tumors with purity < 20% the absolute tolerances are increased.
- Start from most confident germline diploid segment (highest tumor depth window count) and extend outwards in both directions until we reach a segment outside of tolerance. Then move on to next most confident unsmoothed germline diploid segment.
- It is possible to merge in (multiple) segments that would otherwise be outside of tolerances if:
- The total dubious region is sufficiently small (< 30 depth window count or < 50 depth window count if approaching centromere); and
- The dubious region does not end because of a structural variant; and
- The dubious region ends at a centromere, telomere or a segment that is within tolerances.
When merging segments, the depth window count (number of COBALT windows) of each segment is used as a proxy for confidence and is used to calculate a weighted average of the copy number. Similarly, the BAF count is used to calculate the weighted average BAF. The min and max start of the combined region is the minimum from each segment.
Regions that are non-diploid in the germline are typically smoothed over, thus the copy number profile represents the somatic copy number without influence from the germline. However, where smoothing is otherwise not possible PURPLE can sometimes use the reference normalised copy number for this region, ie, the copy number as adjusted for the actual reference read ratio rather than the ideal read ratio. For this to occur, the non-diploid region must:
- Be directly adjacent to a structural variant but not a centromere;
- Not be excessively noisy in the germline (reference read ratio < 2.2x expected);
- Have some depth window support from COBALT;
- be amplified in the tumor relative to the normal, ie, observed tumor ratio > observed normal ratio.
Consecutive non-diploid regions un-interrupted by a structural variant will be merged together.
Where clusters of SVs exist which are closer together than our read depth ratio window resolution of 1,000 bases, the segments in between will not have any copy number information associated with them. We use the junction copy number of the structural variants to resolve this.
The outermost segment of any SV cluster will be associated with a structural variant whose junction copy number can be determined from the adjacent copy number region and the VAF of the SV. Note that if we are inferring from a lower copy number region into a higher one and the VAF is > 0.75 then we use the read depth rather than the VAF to infer a junction copy number. We use the average copy number and read depth of the sample to do estimate junction copy number
Given a SV junction copy number, we use orientation of the structural variant to calculate the change in copy number across the SV and hence the copy number of the outermost unknown segment. We repeat this process iteratively and infer the copy number of all regions within a cluster.
When the entire short arm of a chromosome is lacking copy number information (and always on chromosome 13,14,15,21, or 22), the copy number of the long arm is extended to the short arm.
Once copy number region smoothing and inference is complete, it is possible there will be regions without BAF points which will result in a unknown allele specific copy number, since BAF coverage of the genome is limited and many copy number regions can be very small.
For these regions, we infer a BAF and allele specific copy number of one or more consecutive regions with unknown BAF by first examining neighbouring regions with known allele specific copy number and inferring based on the observed copy number changes to the unknown regions. Where possible, we assume that only one allele changes copy number in a set of consecutive regions of unknown allele specific copy number. The other allele is held constant.
Which allele copy number to hold remain constant from the neighbouring region depends on a number of rules including on whether the allele specific copy number is known on both sides of the unknown region or only one one side.
If only one side of the unknown region is available then we determine which of the major or minor allele of that neighbour to remain constant with the following logic:
- If the unknown region is tiny (<= 30 bases) and is greater in copy number than the neighbour, then hold the minor allele constant.
- Else, find the nearest copy number region where one allele changed by more than 0.5 copy number and hold constant the allele that did not change.
- Failing everything else, keep the minor allele constant.
If there is neighbouring information on both sides of the unknown region, then the following rules apply to determine which allele copy number to hold constant:
- If the minimum copy number of the unknown region is significantly less (> 0.5) than the major allele of both sides, then keep the minor allele constant.
- If both the major and minor allele of the neighbours are significantly different (> 0.5) but the minor allele of one matches the major allele of the other ( < 0.5) then choose the matching allele copy number as the constant copy number.
- Else, if the major allele of the neighbours is significantly different keep the minor allele constant.
- Else, if the minor allele of the neighbours is significantly different keep the major allele constant.
- Else, if the unknown region is tiny (<= 30 bases), and is greater in copy number than the neighbour with the largest number of BAF observations, then hold constant that neighbours minor allele.
This rule is intended to deal with the very short overlap which can occur at double strand breaks particularly for LINE insertions. - Else, if the unknown region is small (<= 1000 bases) and is flanked by large (> 1,000,000 bases) LOH regions, then hold constant the minor allele from the neighbour with the largest number of BAF observations. This rule is intended to ensure that short templated insertions do not break regions of LOH.
- Else, if the unknown region is bounded by a simple DUP with LOH on both sides, keep the minor allele constant.
- Else, find the nearest region on each side (without crossing the centromere) with a change in minor or major allele. If found, re-apply logic from the first three steps.
- Failing everything else, hold constant the minor allele of the neighbour with the largest number of BAF observations.
At this stage we have determined a copy number and minor allele copy number for every base in the genome
PURPLE attempts to recover entries from a set of lower confidence structural variants if a recovery vcf (parameter: sv_recovery_vcf) is provided.
There are two situations where PURPLE will attempt to recover structural variants. The first is when a copy number segment is unsupported by an existing structural variant. The second is to search for an structural variant which could offset the copy number impact of an existing “unbalanced” structural variant break that has a junction copy number not supported by the copy number change. A structural variant is considered unbalanced if the unexplained copy number change (ie. the junction copy number - copy number change) is greater than 20% of the copy number at the breakpoint and > 0.5. An unbalanced structural variant must also have a min depth window count of 5 in the copy number segments immediately before and after the SV breakpoint.
Eligible recovery candidates must:
- Be within 1kb of the min and max range of an unsupported copy number breakpoint or within 1kb of the unbalanced structural variant. Breakpoints where both ends are within 1kb of a recovery site are
- Not be “minTumorAF” or "DEDUP" filtered in GRIPSS
- Have a minQual > 300 (breakpoints) or 800 (single breakends)
- Have a junction copy number of at least 50% of the unexplained copy number change and of at least 0.5.
In both situations, if no suitable SV candidate is found to help explain the copy number discrepancy, a single ended breakend will be inferred (with type = 'INF') at that position.
Following the successful recovery any structural variants we will rerun the segmentation, copy number smoothing and minor allele copy number smoothing with the updated structural variants to produce a final set of copy number segments and breakpoints. Note that the purity estimation does not change.
PURPLE searches for candidate germline gene deletions based on the combined tumor normal raw segmented copy number files.
For the purposes of purity and ploidy fitting and copy number smoothing each segment is already annotated according to its genotype in the germline based on its observedNormal ratio, ie, one of DIPLOID (0.85-1.15), HET_DELETION (0.1-0.85), HOM_DELETION (<0.1), AMPLIFICATION (1.15-2.2) or NOISE.
Any gene with a HET_DELETION or HOM_DELETION segment overlapping (within +/- 500 bases to allow for depth window resolution) an exonic region is marked as a germline gene deletion.
Deletions are filtered with the following criteria
| Filter | Description |
|---|---|
| minLength | the deleted segment must be >1kb long |
| inconsistentTumorCN | the implied refNormalisedCopyNumber of the deleted segment in the tumor must be less than the major allele copy number +max(20%,0.5) |
| highNormalRatio | the deleted segment must have an observedNormalCopyNumberRatio < 0.65 (ie equivalent to germline copyNumber < 1.3) |
| cohortFrequency | the deleted segment is observed in > 3 samples in our cohort |
PURPLE will set a FAIL QC status in 2 cases:
- FAIL_CONTAMINATION - if measured contamination in the tumor (by Amber) is >10%
- FAIL_NO_TUMOR - if no evidence of tumor is found in the sample
PURPLE may also report a warning if one of the following conditions is met:
- WARN_DELETED_GENES - if the number of homozygously deleted genes (excluding chr Y) in the sample is > 280. This sometimes occurs in samples with very high MB scale GC Bias, and particularly affects high GC content regions such as CHR 19. It may also indicate a poor fit.
- WARN_HIGH_COPY_NUMBER_NOISE - if the number of copy number segments unsupported on both sides is >220. This can occur due to GC bias on both MB scale and KB scale and also due to other artefacts which may cause short regions to appear highly amplified.
- WARN_GENDER_MISMATCH - if amber and cobalt report different genders
- WARN_LOW_PURITY - if purity is less than 20%
If no warning or fail criteria is met, PURPLE will set qcStatus = PASS
If a somatic VCF is supplied to PURPLE each variant is enriched with the following fields:
- PURPLE_CN: Purity adjusted copy number surrounding variant location
- PURPLE_MACN: Purity adjusted minor allele copy number surrounding variant location
- PURPLE_AF: Purity adjusted allelic frequency of variant
- PURPLE_VCN: Purity adjusted copy number of variant
- SUBCL: Subclonal likelihood between 0 and 1
- KT: Forward/reverse kataegis id
- BIALLELIC: Flag to indicate variant is biallelic
More detailed descriptions of the kataegis, clonality and biallelic status are found below.
Somatic variants of type C>T and C>G in a TpCpN context are annotated as showing Kataegis (Nik Zainal et al., 2012) if there are three or more mutations of that type, strand and context localised within a region with an average inter-mutation distance of <= 1kb. The annotation describes the strand it was found on along with an id and is shared by grouped variants.
For each point mutation we determined the clonality and biallelic status by comparing the estimated number of copies of the variant to the local copy number at the exact base of the variant. The copy number of each variant is calculated by adjusting the observed VAF by the purity and then multiplying by the local copy number to work out the absolute number of chromatids that contain the variant.
To determine whether a mutation should be marked as biallelic (i.e. no wild type remaining), there are two cases.
If the local minor allele copy number is less than 0.5, then the mutation is marked as biallelic if Variant copy number > local copy number - 0.5. The 0.5 tolerance is used to allow for the binomial distribution of VAF measurements for each variant. For example, if the local copy number is 2 and the local minor allele copy number is 0, then any somatic variant with estimated variant copy number > 1.5 is marked as biallelic.
If the local minor allele copy number is at least 0.5, then an additional check is done. In this case a biallelic state is only possible if the minor allele copy number is measured incorrectly or the mutation has developed independently on both alleles. Such independent identical mutations are not very likely, so when the local minor allele copy number is at least 0.5 a mutation is marked biallelic if both:
- Variant copy number > local copy number - 0.5.
- The probability to see at least the observed number of reads with the mutation, assuming that the variant only exists on the major allele, is at most 0.5%.
- More precisely:
1 - Poisson(AlleleReadCount / variantCN * [CN – min(1,minorAlleleCN)], AlleleReadCount-1)<0.005, wherePoissonis the Poisson cumulative probability density function.
- More precisely:
For each variant we also determine a probability that it is subclonal. This is achieved via a two-step process.
First, we fit the somatic variant copy numbers for each sample into a set of clonal and subclonal peaks.
We apply an iterative algorithm to find peaks in the variant copy number distribution:
- Determine the peak by finding the highest density of variants within +/- 0.1 of every 0.01 copy number bucket.
- Sample the variants within a 0.05 variant copy number range around the peak.
- For each sampled variant, use a binomial distribution to estimate the likelihood that the variant would appear in all other 0.05 copy number buckets.
- Sum the expected variants from the peak across all copy number buckets and subtract from the distribution.
- Repeat the process with the next peak
This process yields a set of variant copy number peaks, each with a copy number and a total density (i.e. count of variants). To avoid overfitting small amounts of noise in the distribution, we filter out any peaks that account for less than 40% of the variants in the copy number bucket at the peak itself. After this filtering we scale the fitted peaks by a constant so that the sum of fitted peaks = the total variant count of the sample. We mark a peak as subclonal if the peak variant copy number < 0.85. We also calculate the subclonal likelihood for each individual variant as the proportion of variants in that same copy number bucket fitted as belonging to a subclonal peak.
In tumor only mode, for each variant a set of expected somatic and germline VAF are calculated using the purity and the assumption that for somatic variants that the VCN = {minor allele, major allele or <=1} and that for germline variants the variant is either homozygous or if heterozygous shares the VCN of either the major or minor allele in the tumor. The minimum distance to each of the expected germline and somatic vaf sets is calculated and annotated as VAF_DIS_MIN in the vcf. The variant is assigned a likelihood of being somatic (SOM_LH={HIGH;MED;LOW}) based on the following logic:
HIGH: abs(somatic_vaf_distance) - abs(germline_vaf_dist) < -0.05 OR IS HOTSPOT
LOW: abs(somatic_vaf_distance) - abs(germline_vaf_dist) > 0.08
MED: all other
If a germline VCF is supplied to PURPLE each variant is enriched with the following fields:
- PURPLE_CN: Purity adjusted copy number surrounding variant location
- PURPLE_MACN: Purity adjusted minor allele copy number surrounding variant location
- PURPLE_AF: Purity adjusted allelic frequency of variant
- PURPLE_VCN: Purity adjusted copy number of variant
- BIALLELIC: Flag to indicate variant is biallelic
- GT: Genotype of variant (applied to germline sample only)
- PATH: Pathogenicity of variant
- REPORTED: Will contribute in the driver catalog
More detailed descriptions of the PATH and GT fields are found below.
The pathogenicity enrichment requires the clinvar CLNSIG and CLNSIGCONF annotations. These are consolidated into a single interpretation by taking the strongest signal after ignoring Uncertain_significance.
If both benign and pathogenic signals exist the pathogenicity is set to CONFLICTING.
Regardless of the clinvar signals, a variant will be set to BENIGN_BLACKLIST if it contains either of the BLACKLIST_BED or BLACKLIST_VCF flags.
Valid values are PATHOGENIC, LIKELY_PATHOGENIC, BENIGN, LIKELY_BENIGN, BENIGN_BLACKLIST, CONFLICTING, UNKNOWN.
The genotype enrichment can set the GT field of the germline sample to 0/1 (HET), 1/1 (HOM) or leave it unchanged as ./. and filter the variant as LOW_VAF or LOW_TUMOR_VCN. A variant is filtered as LOW_VAF if AltReadCount < 0.3*TotalReadCount AND POISSON.DIST(totalReadCount-AltReadCount,TotalReadCount/2,TRUE) < 0.002. A variant is filtered as LOW_TUMOR_VCN if the quality is below 120 for HOTSPOT or 200 for PANEL and the variant and the implied variant copy number (VCN) in the tumor is < 0.5.
Alternatively, the variant GT will be set to 1/1 (HOM) if (totalReadCount==AltReadCount) OR (AltReadCount > 0.75*TotalReadCount AND POISSON.DIST(totalReadCount-AltReadCount,TotalReadCount/2,TRUE) < 0.005) in BOTH tumor and normal and 0/1 (HET) otherwise. AdjustedVAF is set to 1 for Homozygous germline variants.
The reported flag controls if the variant should appear in the driver catalog. In the gene panel configuration reporting may be configured per gene independently for known hotspots and also other likely pathogenic germline variants (specifically nonsense/frameshift or splice variants that are not annotated as BENIGN or LIKELY BENIGN in CLINVAR). For both types of events, the configuration allows the following per gene reporting options:
NONE- never report for this geneANY- always report events for this geneWILDTYPE_LOST- report only if the wildtype is predicted to be lost in the tumor for this gene either via LOH or a somatic 2nd hitVARIANT_NOT_LOST- report only if the variant is predicted to be NOT lost in the tumor for this gene:
PURPLE builds a catalog of drivers based on a configured gene panel. PURPLE automatically assigns a driver likelihood of 1 to all significant amplifications (minimum exonic copy number > 3 * sample ploidy) and deletions (minimum exonic copy number < 0.5) that are reportable. If the somatic VCF is PAVE annotated, a driver likelihood is calculated for any point mutations in the gene panel.
A detailed description of the driver catalog is available here.
Note that additional restrictions apply on amplification and deletion drivers for samples with QC warnings:
- If warning = WARN_DELETED_GENES or WARN_HIGH_COPY_NUMBER_NOISE, DELs must be supported on both sides by SV OR (supported by SV + CENTROMERE/TELOMERE and be <10M bases).
- If warning = WARN_HIGH_COPY_NUMBER_NOISE, AMPS must be bounded on at least one side by an SV.
PURPLE generates a number of tab separated output files as described in the following sections.
The purity file TUMOR.purple.purity.tsv contains a single row with a summary of the purity fit:
| Column | Description |
|---|---|
| purity | Purity of tumor in the sample |
| normFactor | Internal factor to convert tumor ratio to copy number. |
| score | Score of fit (lower is better) |
| diploidProportion | Proportion of copy number regions that have 1 (+- 0.2) minor and major allele |
| ploidy | Average ploidy of the tumor sample after adjusting for purity |
| gender | One of MALE or FEMALE |
| status | Either PASS or one or more warning or fail status. Warnings include WARN_DELETED_GENES, WARN_HIGH_COPY_NUMBER_NOISE, FAIL_CONTAMINATION, FAIL_NO_TUMOR, WARN_GENDER_MISMATCH or WARN_LOW_PURITY |
| polyclonalProportion | Proportion of copy number regions that are more than 0.25 from a whole copy number |
| minPurity | Minimum purity with score within 10% of best |
| maxPurity | Maximum purity with score within 10% of best |
| minPloidy | Minimum ploidy with score within 10% of best |
| maxPloidy | Maximum ploidy with score within 10% of best |
| minDiploidProportion | Min estimation for diploid proportion |
| maxDiploidProportion | Min estimation for diploid proportion |
| version | Version of PURPLE |
| somaticPenalty | Penalty from somatic variants with implied variant copy numbers that are inconsistent with the minor and major allele copy number |
| wholeGenomeDuplication | True if more than 10 autosomes have major allele copy number > 1.5 |
| msIndelsPerMb | Microsatellite indels per mega base |
| msStatus | Microsatellite status. One of MSI, MSS or UNKNOWN if somatic variants not supplied |
| tml | Tumor mutational load (# of missense variants in sample) |
| tmlStatus | Tumor mutational load status. One of HIGH, LOW or UNKNOWN if somatic variants not supplied |
| tmbPerMb | Tumor mutational burden (#passing variants per Mb) per mega base |
| tmbStatus | Tumor mutational burden status. One of HIGH, LOW or UNKNOWN if somatic variants not supplied. High = > 10 pass variants per Mb |
| svTumorMutationalBurden | Total number of non inferred, non single passing structural variants detected in sample |
| runMode | TUMOR_GERMLINE, TUMOR or GERMLIME, set based on whether a tumor and/or reference sample were supplied |
| targeted | True if Purple was run with target-region files |
The purity QC TUMOR.purple.purity.qc contains the following status values:
| Column | Description |
|---|---|
| QCStatus | As per 'status' as described above |
| Method | One of NORMAL, HIGHLY_DIPLOID, SOMATIC or NO_TUMOR |
| CopyNumberSegments | Total number of copy number segments in sample |
| UnsupportedCopyNumberSegments | Count of copy number segments with no SV support on either side. A high number is an indicator of poor sample quality |
| Purity | As described above |
| AmberGender | Gender from Amber data |
| CobaltGender | Gender from Cobalt data |
| DeletedGenes | Number of genes with copy number < 0.5 |
| Contamination | Rate of contamination in tumor sample as determined by Amber. |
| GermlineAberration | Any germline chromosomal aberrations detected, one or more of: {KLINEFELTER,TRISOMY_X,TRISOMY_21,TRISOMY_13,TRISOMY_18,TRISOMY_15,XYY,MOSAIC_X} |
| AmberMeanDepth | As calculated by Amber |
minDiploidProportion maxDiploidProportion version somaticPenalty wholeGenomeDuplication msIndelsPerMb msStatus tml tmlStatus tmbPerMb tmbStatus svTumorMutationalBurden
The purity range file TUMOR.purple.purity.range.tsv file summarises the best fit per purity sorted by score.
Descriptions of the fields are the same as above.
| purity | normFactor | Score | diploidProportion | ploidy | somaticPenalty |
|---|---|---|---|---|---|
| 0.9800 | 0.6400 | 0.6867 | 0.0199 | 3.1076 | 0.0000 |
| 0.9900 | 0.6400 | 0.6888 | 0.0199 | 3.0965 | 0.0000 |
| 1.0000 | 0.6300 | 0.6928 | 0.0199 | 3.1345 | 0.0000 |
The copy number file TUMOR.purple.cnv.somatic.tsv contains the copy number profile of all (contiguous) segments of the tumor sample:
| Column | Description |
|---|---|
| chromosome | Chromosome of copy number segment |
| start | Start base of copy number segment |
| end | End base of copy number segment |
| copyNumber | Fitted absolute copy number of segment adjusted for purity and ploidy |
| bafCount | Count of AMBER baf points covered by this segment |
| observedBAF | Combined reference and tumor BAF in TUMOR sample unadjusted for purity and ploidy |
| baf | Tumor BAF after adjusted for purity and ploidy |
| segmentStartSupport | The type of structural variant support for the copy number breakpoint at start of region. Allowed values: (CENTROMERE, TELOMERE,INV,DEL,DUP,BND - translocation, SGL - single breakend SV support, NONE - no SV support for CN breakpoint, MULT - multiple SV support at exact breakpoint) |
| segmentEndSupport | The type of structural variant support for the copy number breakpoint at end of region. Allowed values as per SegmentStartSupport. |
| method | Method used to determine the copy number of the region. Allowed values: (BAF_WEIGHTED - average of all depth windows for the region ,STRUCTURAL_VARIANT - inferred using junction copy number of flanking SVs ,LONG_ARM - inferred from the long arm,GERMLINE_AMPLIFICATION - inferred using special logic to handle regions of germline amplification) |
| depthWindowCount | Count of COBALT windows covered by this segment |
| gcContent | Proportion of segment that is G or C |
| minStart | Minimum start location of this segment if there is any uncertainty. |
| maxStart | Maximum start location of this segment if there is any uncertainty. |
| minorAlleleCopyNumber | Copy number of minor allele adjusted for purity |
| majorAlleleCopyNumber | Copy number of major allele adjusted for purity |
The gene copy number file TUMOR.purple.cnv.gene.tsv summarises copy number alterations of each gene in the HMF gene panel:
| Column | Description |
|---|---|
| chromosome | Chromosome of gene |
| start | Start location of gene transcript |
| end | End location of gene transcript |
| gene | Name of gene as per Ensembl and HGNC |
| minCopyNumber | Minimum copy number found in the gene exons |
| maxCopyNumber | Maximum copy number found in the gene exons |
| somaticRegions | Count of somatic copy number regions this gene spans |
| transcriptId | Ensembl transcript ID |
| isCanonical | True/false |
| chromosomeBand | Chromosome Band of the gene |
| minRegions | Number of somatic regions inside the gene that share the min copy number |
| minRegionStart | Start base of the copy number region overlapping the gene with the minimum copy number |
| minRegionEnd | End base of the copy number region overlapping the gene with the minimum copy number |
| minRegionStartSupport | Start support of the copy number region overlapping the gene with the minimum copy number |
| minRegionEndSupport | End support of the copy number region overlapping the gene with the minimum copy number |
| minRegionMethod | Method used to determine copy number of the copy number region overlapping the gene with the minimum copy number |
| minMinorAlleleCopyNumber | Minimum allele copy number found over the gene exons - useful for identifying LOH events |
The driver catalog file TUMOR.driver.catalog.somatic.tsv contains significant amplifications (minimum exonic copy number > 3 * sample ploidy) and deletions (minimum exonic copy number < 0.5) that occur in the HMF gene panel.
If the supplied somatic VCF has been enriched with PAVE, the driver catalog file will also include a likelihood of any point mutations in the gene panel.
If a germline variant VCF is supplied then Purple will also produce a driver catalog for those, named TUMOR.driver.catalog.germline.tsv.
A detailed description of the driver catalog is available here.
| Column | Description |
|---|---|
| chromosome | Chromosome of gene |
| chromosomeBand | Chromosome band of driver |
| gene | Name of gene |
| transcriptId | Ensembl transcript ID |
| isCanonical | True/false |
| driver | Driver type [AMP, DEL, MUTATION] |
| category | Gene driver type [ONCO, TSG] |
| likelihoodMethod | Method used to determine likelihood [AMP, DEL, BIALLELIC, DNDS, HOTSPOT, INFRAME] |
| driverLikelihood | Likelihood that gene is a driver |
| missense | Number of missense variants in gene |
| nonsense | Number of nonsense variants in gene |
| splice | Number of splice variants in gene |
| inframe | Number of inframe variants in gene |
| frameshift | Number of frameshift variants in gene |
| biallelic | True if any variants in the gene are biallelic |
| minCopyNumber | Minimum copy number found in the gene exons |
| maxCopyNumber | Maximum copy number found in the gene exons |
If structural or somatic VCF files have been supplied to PURPLE then corresponding VCFs will be written to the output directory enriched with purity information.
The output VCF TUMOR.purple.sv.vcf.gz will contain all (filtered and unfiltered) entries from the input structural variant VCF and also any entries recovered from the recovery VCF
enriched with the following fields:
| Field | Count | Description |
|---|---|---|
| PURPLE_JCN | 1 | Purity adjusted junction copy number of variant |
| PURPLE_AF | 1 or 2 | Purity adjusted allele frequency at each breakend |
| PURPLE_CN | 1 or 2 | Purity adjusted copy number at each breakend |
| PURPLE_CN_CHANGE | 1 or 2 | Purity adjusted change in copy number at each breakend |
| RECOVERED | 0 | Flag to indicate entry has been recovered |
| RECOVERY_METHOD | 1 | Method used to recover, one of UNBALANCED_SV_START, UNBALANCED_SV_END, UNSUPPORTED_BREAKEND_START, UNSUPPORTED_BREAKEND_END |
| RECOVERY_FILTER | n | Filter prior to recovery |
| REFG | 1 | Ref genome surrounding break point |
The output VCF TUMOR.purple.somatic.vcf.gz will contain all (filtered and unfiltered) entries from the input somatic VCF enriched with the following fields:
| Field | Count | Description |
|---|---|---|
| PURPLE_VCN | 1 | Purity adjusted number of copies of variant |
| PURPLE_AF | 1 | Purity adjusted allelic frequency of variant |
| PURPLE_CN | 1 | Purity adjusted copy number surrounding variant location |
| PURPLE_MACN | 1 | Purity adjusted minor allele copy number surrounding variant location |
| PURPLE_GERMLINE | 1 | Germline classification surrounding variant location, one of HOM_DELETION, HET_DELETION, AMPLIFICATION, NOISE, DIPLOID, UNKNOWN |
| BIALLELIC | 1 | Flag to indicate variant is biallelic |
| REP_S | 1 | Repeat sequence |
| REP_C | 1 | Repeat sequence count |
| TNC | 1 | Tri-nucleotide context |
| MH | 1 | Microhomology |
| KT | 1 | Forward/reverse kataegis id |
| SUBCL | 1 | Subclonal likelihood between 0 and 1 |
Data for the CIRCOS plots is found in the output_dir/circos directory even if the circos parameter is not supplied.
This allows the figures to be generated after PURPLE has finished from the command line, eg:
~/hmf/tools/circos-0.69-6/bin/circos -nosvg -conf ~/hmf/analysis/COLO829/purple/circos/COLO829T.input.conf -outputdir ~/hmf/analysis/COLO829T/purple/plot -outputfile COLO829T.input.png
~/hmf/tools/circos-0.69-6/bin/circos -nosvg -conf ~/hmf/analysis/COLO829/purple/circos/COLO829T.circos.conf -outputdir ~/hmf/analysis/COLO829T/purple/plot -outputfile COLO829T.circos.png
If the circos parameter is supplied, these input and output diagrams will be automatically created in the output_dir/plot directory.
The first figure shows the input to PURPLE from AMBER and COBALT.
The second figure shows the output from PURPLE.
A typical input figure is shown below:
The outer circle shows the COBALT ratios of the reference and tumor samples in green and blue respectively. Note the reference ratios are after GC and diploid normalization have been applied. The tumor ratios are after GC normalization has been applied.
The inner circle shows the raw AMBER BAF points in orange.
A typical output figure is shown below:
The outer first circle shows the chromosomes. The darker shaded areas represent large gaps in the human reference genome: i.e. regions of centromeres, heterochromatin & missing short arms.
The second circle shows the somatic variants (incl. exon, intron and intergenic regions). Somatic variants are further divided into an outer ring of single nucleotide polymorphism (SNP) allele frequencies and an inner ring of short insertion/deletion (INDEL) locations. SNP allele frequencies have been corrected for tumor purity and scale from 0 to 100%. Each dot represents a single somatic variant. SNPs are colored according to the type of base change (e.g. C>T/G>A in red) and are in concordance with the coloring used in Alexandrov et al. 2013 Nature paper that describes the use of mutational signatures. INDELs are colored yellow and red for insertions and deletions respectively.
The third circle shows all observed tumor purity adjusted copy number changes, including both focal and chromosomal somatic events. Absolute copy number less than 2 is indicated in red, green shows regions of copy number greater than 2. The scale ranges from 0 (complete loss) to 6 (high level gains). If the absolute copy number is > 6 it is shown as 6 with a green dot on the diagram.
The fourth circle represents the observed 'minor allele copy numbers’ across the chromosome. The range of the chart is from 0 to 3. The expected normal minor allele copy number is 1, and anything below 1 is shown as a loss (orange) and represents a LOH event. Minor allele copy numbers above 1 (blue) indicate amplification events of both A and B alleles at the indicated locations.
The innermost circle displays the observed structural variants within or between the chromosomes. Translocations are indicated in blue, deletions in red, insertions in yellow, tandem duplications in green and inversions in black.
Charts are generated with R using the data found in the output directory. They are created from the copyNumberPlots.R script and can be regenerated by supplying the tumor name, PURPLE output directory and desired location to create the figures, eg.
Rscript copyNumberPlots.R COLO829T ~/hmf/COLO829T/purple ~/hmf/COLO829T/purple/plot
The following 'sunrise' chart shows the range of scores of all examined solutions of purity and ploidy. Crosshairs identify the best purity / ploidy solution. Other viable solutions are shown in blue.
The contribution of each fitted segment to the final score of the best fit is shown in the following figure. Each segment is divided into its major and minor allele copy number. The area of each circle shows the weight (AMBER baf count) of each segment.
The following figures shows the AMBER BAF count weighted distribution of copy number and minor allele copy number throughout the fitted segments. Copy numbers are broken down by colour into their respective minor allele copy number (MAP) while the minor allele copy number figure is broken down by copy number.
If a somatic variant VCF has been supplied, a similar figure will be produced showing the somatic variant copy number broken down by copy number as well as rainfall plot with kataegis clusters highlighted grey:
The following diagram illustrates the clonality model of a typical sample.
The top figure shows the histogram of somatic variant copy number for all SNV and INDEL in blue. Superimposed are peaks in different colours fitted from the sample as described above while the black line shows the overall fitted copy number distribution. Red filled peaks are below the 0.85 subclonal threshold.
We can determine the likelihood of a variant being subclonal at any given variant copy number as shown in the bottom half of the figure.
In Targeted Mode from release 5.34, Purple provides a HRD+ or HRD- prediction akin to the CHORD module.
This HRD classifier is still in experimental stage due to the small number of training and validation samples available. This tool will be continuously improved as more HRD+ samples are received.
Purity & Ploidy fitting:
- Somatic penalty - Currently this depends on the upper tail of the distribution of VAFs, which may pick up noise and tend to apply a too agressive penalty. Better would be to strongly penalise clearly defined peaks of variants with variant copy numbers that are inconsistent with the fitted major allele copy number at the location.
- Fit resolution - currently set to 1%. Setting to 0.5% or lower may allow better fitting at lower purities including potentially <0.08
- TUMOR ONLY fitting for Hgh Purity samples - High / low BAF points currently get ingnored (as they may be homozygous in germline), but long regions of homozygous or near homozygous points are very convincning evidence of high purity and should be captured.
- Imputation - Used population phased BAF points in segmentation would allow better subclonal calling and calling at TF < 0.08
Other functionality:
- MOSAIC Y LOSS - Common in adult males. Should be detected in germline similar to MOSAIC X. Currently all males are assumed to have 1 copy in germline, which may lead to copy number being under estimated in tumor.
- Pathogenic GL DUP - currently not called
- Subclonal likelihood - Subclonal likelihood can be very volatile if subclonal peak and clonal peak hardly overlap. In this case variants in the middle should be highly uncertain (ie. likelihood -> 0.5)
- TCR CN estimate - TCR regions currently excluded from the fit due to CN effects of T cell VDJ rearrangements. We should use to estimate T cell infiltration from CN ratios