seqCAT: The High Throughput Sequencing Cell Authentication Toolkit
Introduction
This vignette describes the use of the seqCAT package for authentication, characterisation and evaluation of two or more High Throughput Sequencing samples (HTS; RNA-seq or whole genome sequencing). The principle of the method is built upon previous work, where it was demonstrated that analysing the entirety of the variants found in HTS data provides unprecedented statistical power and great opportunities for functional evaluation of genetic similarities and differences between biological samples (Fasterius et al. 2017; Fasterius and Szigyarto 2018).
The seqCAT package work by creating Single Nucelotide Variant (SNV) profiles of every sample of interest, followed by comparisons between each set to find overall genetic similarity, in addition to detailed analyses of the differences. By analysing your data with this workflow you will not only be able to authenticate your samples to a high degree of confidence, but you will also be able to investigate what genes and transcripts are affected by SNVs differing between your samples, what biological effect they will have, and more. The workflow consists of three separate steps:
1. Creation of SNV profiles
2. Comparisons of SNV profiles
3. Authentication, characterisation and evaluation of profile comparisonsEach step has its own section(s) below demonstrating how to perform the analyses. Input data should be in the form of VCF files, i.e output from variant callers such as the Genome Analysis ToolKit and optionally annotated with software such as SnpEff.
Installation
The latest stable release of this package can be found on Bioconductor and installed with:
This will also install any missing packages requires for full
functionality, should they not already exist in your system. If you
haven’t installed Bioconductor, you can do so by simply calling
BiocManager::install() without specifying a package, and it
will be installed for you. You can read more about this at
Bioconductor’s installation
page. You can also find the development version of seqCAT on GitHub, which can be
installed like so:
Creation of SNV profiles
The first step of the workflow is to create the SNV profile of each
sample, which can then be compared to each other. The creation of a SNV
profile includes filtering of low-confidence variants, removal of
variants below a sequencing depth threshold (10 by
default), de-duplication of variants and an optional removal of
mitochondrial variants (TRUE by default). For annotated VCF
files, only records with the highest SNV impact (i.e. impact
on protein function) for each variant is kept, as they are most likely
to affect the biology of the cells.
Create individual profiles
Throughout this vignette we will be using some example data,
example.vcf.gz, which comes from the initial publication of
the general process of this method (Fasterius
et al. 2017). It is a simplified multi-sample VCF file on a
subset of chromosome 12 (containing all variants up to position
25400000, in order to keep the file size low) for three
different colorectal cancer cell lines: HCT116, HKE3
and RKO. The first step is to load the seqCAT
package and to create SNV profiles for each sample:
# Load the package
library("seqCAT")
# List the example VCF file
vcf <- system.file("extdata", "example.vcf.gz", package = "seqCAT")
# Create two SNV profiles
hct116 <- create_profile(vcf, "HCT116")
head(hct116)## chr pos rsID gene ENSGID ENSTID REF
## 1 12 80385 rs370087224 ABC7-42389800N19.1 ENSG00000226210 ENST00000400706 C
## 2 12 80399 None ABC7-42389800N19.1 ENSG00000226210 ENST00000400706 G
## 3 12 80422 rs373297723 ABC7-42389800N19.1 ENSG00000226210 ENST00000400706 G
## 4 12 80729 rs375960073 ABC7-42389800N19.1 ENSG00000226210 ENST00000400706 A
## 5 12 83011 rs370570891 ABC7-42389800N19.1 ENSG00000226210 ENST00000400706 T
## 6 12 83012 rs374646339 ABC7-42389800N19.1 ENSG00000226210 ENST00000400706 C
## ALT impact effect feature biotype DP AD1 AD2 A1
## 1 T MODIFIER intron_variant transcript unprocessed_pseudogene 10 8 2 C
## 2 A MODIFIER intron_variant transcript unprocessed_pseudogene 10 4 6 G
## 3 A MODIFIER intron_variant transcript unprocessed_pseudogene 15 11 4 G
## 4 G MODIFIER intron_variant transcript unprocessed_pseudogene 18 13 5 A
## 5 C MODIFIER intron_variant transcript unprocessed_pseudogene 10 3 7 T
## 6 G MODIFIER intron_variant transcript unprocessed_pseudogene 10 3 7 C
## A2 FILTER warnings sample
## 1 T PASS HCT116
## 2 A PASS HCT116
## 3 A PASS HCT116
## 4 G PASS HCT116
## 5 C PASS HCT116
## 6 G PASS HCT116The SNV profile lists all the variants present in the VCF file, in
addition to any annotations present. This means that information
pertaining to the genomic position (chr and
pos), reference and alternative alleles (REF
and ALT), genotype (A1 and A2)
and depth (DP, variant depth; AD1 and
AD2, allelic depth) are always going to be present in all
profiles. The profiles creates here also contain additional annotations
from SnpEff, such as gene
(ENSGID), variant impact
(impact) and variant accession (rsID).
Variant filtration
The creation of SNV profiles include several optional variant
filtration steps, including criteria for sequencing depth, variant
caller-specific thresholds, mitochondrial variants, variants in
non-standard chromosomes and variants duplicated at either the
gene-level or positional level. The create_profile function
performs all of these by default (with a sequencing depth of at least 10
and de-duplication at the gene-level), but you can omit or change these
as required, like so:
The profile of this sample (RKO) was created with a
non-standard filter for sequencing depth (min_depth = 15),
which should only be done if you want a stricter criteria for your
profile (such as when you’re only interested in higher-than-standard
confidence variants).
You may also choose to not remove variants using the variant
caller-specific filtering criteria by passing
filter_vc = FALSE when creating your profile, although it
is recommended to do so in most cases in order to minimise the number of
false positive variant calls. Mitochondrial variants are removed by
default, but may be kept by passing filter_mt = FALSE; the
same goes for non-standard chromosomes and the filter_ns
parameter.
Duplicate variants can either be removed at the gene-level
(filter_gd = TRUE by default) or at the positional level
(filter_pd = FALSE by default). The former will remove
variants that have more than one entry on a per-gene basis
(i.e. variants that affect more than one transcript for the
same gene), but keep multiple entries for variants affecting more than
one gene; the impact is used to determine which of the same-gene
variants to keep. The latter will remove duplicated variants purely by
their position, regardless of the genes or transcripts they affect. It
is thus important to know what type of downstream analyses you want to
perform at this stage: if analysis of which genes or transcripts are
affected by the variants is desired, duplicates should either be remove
at the gene-level or not at all; if only not, variant duplicates may be
remove at the positional level.
Filtration can also be performed after the initial SNV profile creation, using two separate functions:
Create multiple profiles
The create_profiles function is a convenience wrapper
for create_profile, which will create SNV profiles for each
VCF file in a given input directory and return them as a list. You can
use it for all the VCFs in a directory or a subset specified by a
string, like so:
Create COSMIC profiles
It is also possible to to compare your samples’ variants to some external source. Such a source is the Catalogue of somatic mutations in cancer, or COSMIC. (Forbes et al. 2015) COSMIC has over a thousand cell line-specific mutational profiles as well as a comprehensive list of cancer mutations in across many carcinoma samples, and is thus a very useful resource.
In order to use the COSMIC database, you need to sign up for an
account at their website
and get permission to download their files (which is given free of
charge to academia and non-profit organisation, but requires a
commersial license for for-profit organisations). SeqCAT can analyse
both the cell line-specific (the
CosmicCLP_MutantExport.tsv.gz file) and cancer mutation
data (the CosmicCompleteTargetedScreensMutantExport.tsv.gz
file) that can be found here. As
redistributing this data is not allowed, this package includes an
extremely minimal subset of the original files, only useful for examples
in this vignette and unit testing. Do not use these file for
your own analyses, as your results will neither be complete nor
accurate!
Here we present an example of how to analyse some cell line-specific
COSMIC data. The first thing to check is to see if your specific cell
line is available in the database, which can be accomplished using the
list_cosmic function:
file <- system.file("extdata", "subset_CosmicCLP_MutantExport.tsv.gz",
package = "seqCAT")
cell_lines <- list_cosmic(file)
head(cell_lines)## [1] "639V" "A427" "A549" "AGS" "AMO1" "AN3CA"This gives us a simple vector containing all the available sample names in the COSMIC database (this version of the file is for the GRCh37 assembly). You can search it for a cell line of your choice:
## [1] TRUEAll COSMIC-related functions perform some simplification of sample
names (as there is variation in the usage of dashes, dots and other
symbols), and are case-insensitive. When you have asserted that your
sample of interest is available, you can then read the profile for that
sample using the read_cosmic function:
## chr pos REF ALT A1 A2 gene ENSTID gene_cds_length hgnc_id
## 43 12 25398281 C T C T KRAS ENST00000311936 567 6407
## sample id_sample id_tumour primary_site site_subtype_1
## 43 COSMIC.HCT116 905936 823462 LARGE_INTESTINE colon
## site_subtype_2 site_subtype_3 primary_histology histology_subtype_1
## 43 NS NS carcinoma NS
## histology_subtype_2 histology_subtype_3 genome_wide_screen id cds
## 43 NS NS y COSM532 c.38G>A
## aa description loh grch snp fathmm_prediction fathmm_score
## 43 p.G13D Substitution - Missense u 37 n PATHOGENIC 0.97875
## somatic_status verification_status pubmed_pmid
## 43 Reported in another cancer sample as somatic Verified NA
## id_study institute
## 43 619 Developmental Therapeutics Program
## institute_address catalogue_number sample_source
## 43 National Cancer Institute,Frederick,MD 21701 cell-line
## tumour_origin age
## 43 primary NAYou now have a small, COSMIC SNV profile for your cell line, which you can compare to any other profile you may have data for (more on this below). You can also check how many variants are listed in COSMIC for your particular cell:
## [1] 1Here we only see a single variant for the HCT116 cell line, which is only because of the extreme small subset of the COSMIC databse being used here. HCT116 has, in fact, over 2000 listed COSMIC SNVs, making it one of the more abundantly characterised cell lines available (as most cell lines has only a few hundred SNVs listed in COSMIC). A COSMIC profile of a couple of hundred variants is more common, though, and any analysis based only on COSMIC variants is thus inherently limited.
Working with profiles on disk
While computation time is usually not an issue for simple binary
comparisons (i.e. comparisons with only two samples), this can
quickly become a concern for analyses where samples are compared to
several others (A vs B, A vs C, …, and so on); this is doubly true for
annotated VCF files. It can thus be highly useful to save profiles to
disk in some cases, in order to facilitate re-analysis at a later stage.
This can be done with the write_profile function:
You may also store profiles in several other formats, including BED, GTF and GFF; these are automatically detected based on the filename:
The write_profiles function is a convenience-wrapper
from write_profile, which can save many profiles (stored in
a list) to disk at the same time:
Profiles stored on disk may be read into R again at a later time
using the read_profile function:
The read_profiles function is a convenience-wrapper for
read_profile, which will automatically read all the
profiles present in a given directory (based on the pattern
argument) and return them as a list.
## chr pos rsID gene ENSGID ENSTID REF ALT
## 1 1 16229 None DDX11L1 ENSG00000223972 ENST00000456328 C A
## 2 1 16298 rs200451305 DDX11L1 ENSG00000223972 ENST00000456328 C T
## 3 1 16495 rs141130360 DDX11L1 ENSG00000223972 ENST00000450305 G C
## 4 1 16495 rs141130360 WASH7P ENSG00000227232 ENST00000423562 G C
## 5 1 16534 rs201459529 DDX11L1 ENSG00000223972 ENST00000450305 C T
## 6 1 16534 rs201459529 WASH7P ENSG00000227232 ENST00000423562 C T
## impact effect feature
## 1 MODIFIER downstream_gene_variant transcript
## 2 MODIFIER downstream_gene_variant transcript
## 3 MODIFIER downstream_gene_variant transcript
## 4 MODIFIER intron_variant transcript
## 5 MODIFIER downstream_gene_variant transcript
## 6 MODIFIER intron_variant transcript
## biotype DP AD1 AD2 A1 A2 FILTER warnings sample
## 1 processed_transcript 27 21 6 C A PASS sample1
## 2 processed_transcript 19 8 11 C T PASS sample1
## 3 transcribed_unprocessed_pseudogene 33 24 9 G C PASS sample1
## 4 unprocessed_pseudogene 33 24 9 G C PASS sample1
## 5 transcribed_unprocessed_pseudogene 22 13 9 C T PASS sample1
## 6 unprocessed_pseudogene 22 13 9 C T PASS sample1Comparing SNV profiles
Comparing full profiles
Once each relevant sample has its own SNV profile the comparisons can
be performed. SNV profiles contain most of the relevant annotation data
from the original VCF file, including SNV impacts, gene/transcript IDs
and mutational (rs) ID. The DP (depth) field lists the
total sequencing depth of this variant, while the specific allelic
depths can be found in AD1 and AD2. The
alleles of each variant can be found in A1 and
A2.
Once each profile has been defined, the genotypes of the overlapping
variants between them can be compared using the
compare_profiles function. Only variants found in both
profiles are considered to overlap by default, as similarity
calculations between profiles where some variants only have confident
calls in one of the samples may be inappropriate. An SNV is considered a
match if it has an identical genotype in both profiles.
## chr pos sample_1 sample_2 match rsID gene
## 1 12 80729 HCT116 RKO match rs375960073 ABC7-42389800N19.1
## 2 12 83508 HCT116 RKO match rs374142069 ABC7-42389800N19.1
## 3 12 83560 HCT116 RKO match rs368663404 ABC7-42389800N19.1
## 4 12 83979 HCT116 RKO match rs369733672 ABC7-42389800N19.1
## 5 12 84000 HCT116 RKO match rs374158904 ABC7-42389800N19.1
## 6 12 84096 HCT116 RKO match rs376990822 ABC7-42389800N19.1
## ENSGID ENSTID REF ALT impact effect feature
## 1 ENSG00000226210 ENST00000400706 A G MODIFIER intron_variant transcript
## 2 ENSG00000226210 ENST00000400706 T G MODIFIER intron_variant transcript
## 3 ENSG00000226210 ENST00000400706 G T MODIFIER intron_variant transcript
## 4 ENSG00000226210 ENST00000400706 T C MODIFIER intron_variant transcript
## 5 ENSG00000226210 ENST00000400706 C G MODIFIER intron_variant transcript
## 6 ENSG00000226210 ENST00000400706 C G MODIFIER intron_variant transcript
## biotype DP.HCT116 AD1.HCT116 AD2.HCT116 A1.HCT116 A2.HCT116
## 1 unprocessed_pseudogene 18 13 5 A G
## 2 unprocessed_pseudogene 26 21 5 T G
## 3 unprocessed_pseudogene 21 14 7 G T
## 4 unprocessed_pseudogene 51 42 9 T C
## 5 unprocessed_pseudogene 52 42 10 C G
## 6 unprocessed_pseudogene 65 49 16 C G
## FILTER.HCT116 warnings.HCT116 DP.RKO AD1.RKO AD2.RKO A1.RKO A2.RKO FILTER.RKO
## 1 PASS 15 8 7 A G PASS
## 2 PASS 17 6 11 T G PASS
## 3 PASS 16 4 12 G T PASS
## 4 PASS 23 14 9 T C PASS
## 5 PASS 18 9 9 C G PASS
## 6 PASS 18 10 8 C G PASS
## warnings.RKO
## 1
## 2
## 3
## 4
## 5
## 6The resulting dataframe retains all the information from each input
profile (including any differing annotation, should they exist), and
lists the depths and alleles by adding the sample names as suffixes to
the relevant column names. An optional parameter, mode, can
also be supplied: the default value ("intersection")
discards any non-overlapping variants in the comparison, while setting
it to "union" will retain them.
## chr pos sample_1 sample_2 match rsID gene
## 1 12 80385 HCT116 RKO HCT116_only rs370087224 ABC7-42389800N19.1
## 2 12 80399 HCT116 RKO HCT116_only None ABC7-42389800N19.1
## 3 12 80422 HCT116 RKO HCT116_only rs373297723 ABC7-42389800N19.1
## 4 12 80610 HCT116 RKO RKO_only None ABC7-42389800N19.1
## 5 12 80729 HCT116 RKO match rs375960073 ABC7-42389800N19.1
## 6 12 83011 HCT116 RKO HCT116_only rs374646339 ABC7-42389800N19.1
## ENSGID ENSTID REF ALT impact effect feature
## 1 ENSG00000226210 ENST00000400706 C T MODIFIER intron_variant transcript
## 2 ENSG00000226210 ENST00000400706 G A MODIFIER intron_variant transcript
## 3 ENSG00000226210 ENST00000400706 G A MODIFIER intron_variant transcript
## 4 ENSG00000226210 ENST00000400706 C G MODIFIER intron_variant transcript
## 5 ENSG00000226210 ENST00000400706 A G MODIFIER intron_variant transcript
## 6 ENSG00000226210 ENST00000400706 C G MODIFIER intron_variant transcript
## biotype DP.HCT116 AD1.HCT116 AD2.HCT116 A1.HCT116 A2.HCT116
## 1 unprocessed_pseudogene 10 8 2 C T
## 2 unprocessed_pseudogene 10 4 6 G A
## 3 unprocessed_pseudogene 15 11 4 G A
## 4 unprocessed_pseudogene
## 5 unprocessed_pseudogene 18 13 5 A G
## 6 unprocessed_pseudogene 10 3 7 C G
## FILTER.HCT116 warnings.HCT116 DP.RKO AD1.RKO AD2.RKO A1.RKO A2.RKO FILTER.RKO
## 1 PASS
## 2 PASS
## 3 PASS
## 4 16 11 5 C G PASS
## 5 PASS 15 8 7 A G PASS
## 6 PASS
## warnings.RKO
## 1
## 2
## 3
## 4
## 5
## 6Comparing to COSMIC profiles
If you only want to analyse a subset of your data or as a orthogonal method complementary to others, you could compare your profile to a COSMIC profile. This works in the same way as comparing to another full profile, but gives slightly different output:
## chr pos sample_1 sample_2 match rsID ENSGID
## 1 12 25398281 HCT116 COSMIC.HCT116 match rs112445441 ENSG00000133703
## impact effect feature biotype gene
## 1 MODERATE missense_variant transcript protein_coding KRAS
## ENSTID REF ALT DP.HCT116 AD1.HCT116 AD2.HCT116
## 1 [ENST00000256078,ENST00000311936] C T 180 96 84
## A1.HCT116 A2.HCT116 FILTER.HCT116 warnings.HCT116 A1.COSMIC.HCT116
## 1 C T PASS C
## A2.COSMIC.HCT116 gene_cds_length.COSMIC.HCT116 hgnc_id.COSMIC.HCT116
## 1 T 567 6407
## id_sample.COSMIC.HCT116 id_tumour.COSMIC.HCT116 primary_site.COSMIC.HCT116
## 1 905936 823462 LARGE_INTESTINE
## site_subtype_1.COSMIC.HCT116 site_subtype_2.COSMIC.HCT116
## 1 colon NS
## site_subtype_3.COSMIC.HCT116 primary_histology.COSMIC.HCT116
## 1 NS carcinoma
## histology_subtype_1.COSMIC.HCT116 histology_subtype_2.COSMIC.HCT116
## 1 NS NS
## histology_subtype_3.COSMIC.HCT116 genome_wide_screen.COSMIC.HCT116
## 1 NS y
## id.COSMIC.HCT116 cds.COSMIC.HCT116 aa.COSMIC.HCT116 description.COSMIC.HCT116
## 1 COSM532 c.38G>A p.G13D Substitution - Missense
## loh.COSMIC.HCT116 grch.COSMIC.HCT116 snp.COSMIC.HCT116
## 1 u 37 n
## fathmm_prediction.COSMIC.HCT116 fathmm_score.COSMIC.HCT116
## 1 PATHOGENIC 0.97875
## somatic_status.COSMIC.HCT116
## 1 Reported in another cancer sample as somatic
## verification_status.COSMIC.HCT116 pubmed_pmid.COSMIC.HCT116
## 1 Verified
## id_study.COSMIC.HCT116 institute.COSMIC.HCT116
## 1 619 Developmental Therapeutics Program
## institute_address.COSMIC.HCT116 catalogue_number.COSMIC.HCT116
## 1 National Cancer Institute,Frederick,MD 21701
## sample_source.COSMIC.HCT116 tumour_origin.COSMIC.HCT116 age.COSMIC.HCT116
## 1 cell-line primaryYou can use all the functions for downstream analyses for comparisons with COSMIC data, but your options for functional analyses will be limited, given that the COSMIC database is biased towards well-known and characterised mutations. It is, however, an excellent way to authenticate your cell lines and to assert the status of the mutations that exist in the analysed cells.
Evaluating binary comparisons
Similarity and global statistics
When you have your matched, overlapping SNVs, it’s time to analyse
and characterise them. The first thing you might want to check are the
global similarities and summary statistics, which can be done with the
calculate_similarity function. The concordance
is simply the number of matching genotypes divided by the total number
of overlapping variants, while the similarity score is a
weighted measure of the concordance in the form of a binomial
experiment, taking into account the number of overlapping variants
available:
$$Similarity = \frac{s + a}{n + a + b}$$
… where s is the number of matching genotypes,
n is the total number of overlapping SNVs, a
and b being the parameters used to weigh the concordance in
favour of comparisons with more overlaps. The default parameters of
1 and 5 were selected to yield an equivalent
cutoff to one suggested by Yu et al. (2015), which results in a
lower limit 44 of perfectly matching overlapping variants with a
similarity score of 90. The similarity score is thus a better measure of
biological equivalency than just the concordance.
## sample_1 sample_2 variants_1 variants_2 overlaps matches concordance
## 1 HCT116 RKO 259 259 259 181 69.9
## similarity_score
## 1 68.7Here, you can see a summary of the relevant statistics for your
particular comparison: the number of total variants from each profile
(if the comparison was done with mode = "union", otherwise
this number will just be equivalent to the overlaps), the number of
overlaps between your two samples, the number of matching genotypes,
their concordance as well as their similarity score. The cutoff used by
Yu et al. for cell line authenticity was 90 % for
their 48 SNP panel, something that could be considered the baseline for
this method as well. The score, 68.7, is well below that
cutoff, and we can thus be certain that these two cells are indeed not
the same (as expected). While hard thresholds for similarity are
inadvisable, a general guideline is that comparisons with scores above
90 can be considered similar while those below can be
considered dissimilar. While a score just below 90 does not
mean that the cells definitely are different, it does mean that
more rigorous evaluation needs to be performed in order to ensure their
biological equivalency. Are there specific genes or regions that are of
special interest, for example? If so, it might be informative to
specifically investigate the similarity there (more on this below).
You may additionally change the parameters of the score (if you, for
example, want a stricter calculation). You may also supply the
calculate_similarity function with an existing dataframe
with summary data produced previously, in order to aggregate scores and
statistics for an arbitrary number of comparisons.
# Create and read HKE3 profile
hke3 <- create_profile(vcf, "HKE3")
# Compare HCT116 and HKE3
hct116_hke3 <- compare_profiles(hct116, hke3)
# Add HCT116/HKE3 similarities to HCT116/RKO similarities
similarities <- calculate_similarity(hct116_hke3, similarity, b = 10)
similarities## sample_1 sample_2 variants_1 variants_2 overlaps matches concordance
## 1 HCT116 RKO 259 259 259 181 69.9
## 2 HCT116 HKE3 493 493 493 475 96.3
## similarity_score
## 1 68.7
## 2 94.4Notice that the new similarities dataframe contains both
the comparisons of HCT116/RKO and HCT116/HKE3, and we can clearly see
that HCT116 and HKE3 are indeed very similar, as expected (HKE3 was
derived from HCT116). This is true even when using a higher value for
the b parameter. Any number of samples can be added using
the calculate_similarity function, for use in further
downstream analyses.
Evaluation of SNV impacts
An SNV’s impact
represent the putative effect that variant may have on the function of
the resulting protein, and ranges from HIGH through MODERATE, LOW and
MODIFIER, in decreasing order of magnitude. HIGH impact variants may,
for example, lead to truncated proteins due to the introduction of a
stop codon, while MODIFIER variants have little to no effect on the
protein at all. While there is no guarantee that a specific phenotype
arises from a HIGH rather than a MODERATE impact variant (for example),
it may be informative to look at the impact distribution of the
overlapping SNVs between two profiles. This can easily be performed by
the plot_impacts function:
## Warning: `separate_()` was deprecated in tidyr 1.2.0.
## ℹ Please use `separate()` instead.
## ℹ The deprecated feature was likely used in the seqCAT package.
## Please report the issue to the authors.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
This function takes a comparison dataframe as input and plots the
impact distribution of the overlapping variants. It has a number of
arguments with defaults, such as if you want to add text with the actual
numbers to the plot (annotate = TRUE by default), if you
want to show the legend (legend = TRUE by default) and what
colours you want to plot the match-categories with
(palette = c("#0D2D59", "#1954A6") by default, two shades
of blue). We can see that most of the SNVs are present in the MODIFIER
impact category, and that there is not a single mismatched HIGH impact
SNV. (You can also visualise the impact distribution between your sample
and the COSMIC database in exactly the same way.)
You might also want to look at only a subset of variants, e.g. only the variants with HIGH or MODERATE impacts, which is easily achieved with some data manipulation:
hct116_rko_hm <- hct116_rko[hct116_rko$impact == "HIGH" |
hct116_rko$impact == "MODERATE", ]
nrow(hct116_rko_hm)## [1] 19Evaluation of specific chromosomes, regions, genes and transcripts
You might be interested in a specific chromosome or a region on a chromosome, and it might be useful to work with data for only that subset. This operation is easily performed on a comparison dataframe:
hct116_rko_region <- hct116_rko[hct116_rko$chr == 12 &
hct116_rko$pos >= 25000000 &
hct116_rko$pos <= 30000000, ]
head(hct116_rko_region)## chr pos sample_1 sample_2 match rsID gene ENSGID
## 247 12 25358650 HCT116 RKO match rs12245 LYRM5 ENSG00000205707
## 248 12 25358828 HCT116 RKO match rs12587 LYRM5 ENSG00000205707
## 249 12 25358943 HCT116 RKO match rs8720 LYRM5 ENSG00000205707
## 250 12 25358969 HCT116 RKO match rs1137196 LYRM5 ENSG00000205707
## 251 12 25359328 HCT116 RKO match rs1137189 LYRM5 ENSG00000205707
## 252 12 25359352 HCT116 RKO match rs1137188 LYRM5 ENSG00000205707
## ENSTID REF ALT impact effect
## 247 [ENST00000381356,ENST00000557540] A T MODIFIER downstream_gene_variant
## 248 [ENST00000381356,ENST00000557540] T G MODIFIER downstream_gene_variant
## 249 [ENST00000381356,ENST00000557540] T C MODIFIER downstream_gene_variant
## 250 [ENST00000381356,ENST00000557540] T G MODIFIER downstream_gene_variant
## 251 [ENST00000381356,ENST00000557540] A T MODIFIER downstream_gene_variant
## 252 [ENST00000381356,ENST00000557540] G A MODIFIER downstream_gene_variant
## feature biotype DP.HCT116 AD1.HCT116 AD2.HCT116 A1.HCT116
## 247 transcript protein_coding 351 196 155 A
## 248 transcript protein_coding 382 224 158 T
## 249 transcript protein_coding 380 223 157 T
## 250 transcript protein_coding 306 184 122 T
## 251 transcript protein_coding 436 282 154 A
## 252 transcript protein_coding 407 242 165 G
## A2.HCT116 FILTER.HCT116 warnings.HCT116 DP.RKO AD1.RKO AD2.RKO A1.RKO
## 247 T PASS 414 217 197 A
## 248 G PASS 422 244 178 T
## 249 C PASS 420 238 182 T
## 250 G PASS 349 200 149 T
## 251 T PASS 508 297 211 A
## 252 A PASS 507 270 237 G
## A2.RKO FILTER.RKO warnings.RKO
## 247 T PASS
## 248 G PASS
## 249 C PASS
## 250 G PASS
## 251 T PASS
## 252 A PASSYou might also be interested in a specific gene or transcript, of special importance to your study:
hct116_rko_eps8_t <- hct116_rko[hct116_rko$ENSTID == "ENST00000281172", ]
hct116_rko_vamp1 <- hct116_rko[hct116_rko$ENSGID == "ENSG00000139190", ]
hct116_rko_ldhb <- hct116_rko[hct116_rko$gene == "LDHB", ]
head(hct116_rko_ldhb)## chr pos sample_1 sample_2 match rsID gene ENSGID
## 243 12 21788465 HCT116 RKO mismatch None LDHB ENSG00000111716
## 244 12 21797029 HCT116 RKO match rs1650294 LDHB ENSG00000111716
## ENSTID REF ALT impact
## 243 [ENST00000350669,ENST00000542765] G T MODIFIER
## 244 [ENST00000350669,ENST00000539782] A G LOW
## effect feature
## 243 [3_prime_UTR_variant,non_coding_exon_variant] transcript
## 244 [sequence_feature,synonymous_variant] [helix,transcript]
## biotype DP.HCT116 AD1.HCT116 AD2.HCT116 A1.HCT116
## 243 [protein_coding,retained_intron] 1353 754 599 G
## 244 protein_coding 5157 2 5155 G
## A2.HCT116 FILTER.HCT116 warnings.HCT116 DP.RKO AD1.RKO AD2.RKO A1.RKO
## 243 T PASS 1347 1347 G
## 244 G PASS 4253 2 4251 G
## A2.RKO FILTER.RKO warnings.RKO
## 243 G PASS
## 244 G PASS WARNING_TRANSCRIPT_NO_STOP_CODONHere we see two mutations in the LDHB gene, one mismatching MODIFIER
variant and one matching LOW variant. This is a good approach to check
for known mutations in your dataset. For example, the HCT116 cell line
is supposed to have a KRASG13D mutation. We might look for
this using its known rsID or position:
hct116_rko_kras <- hct116_rko[hct116_rko$rsID == "rs112445441", ]
hct116_rko_kras <- hct116_rko[hct116_rko$chr == 12 &
hct116_rko$pos == 25398281, ]
nrow(hct116_rko_kras)## [1] 0The reason that we don’t find this particular variant in the HCT116
vs. RKO comparison is that it is not present in the RKO profile, either
because it isn’t a mutation in RKO or because there was no confident
variant call for that particular position. The
compare_profiles function only looks at overlapping
positions by default, so we will have to look at the individual profiles
instead. seqCAT has two functions to help with this:
list_variants and plot_variant_list:
The list_variants function looks for the genotypes of
each specified variant in each provided SNV profile. First, let’s create
a small set of interesting variants we want to look closer at:
known_variants <- data.frame(chr = c(12, 12, 12, 12),
pos = c(25358650, 21788465, 21797029, 25398281),
gene = c("LYRM5", "LDHB", "LDHB", "KRAS"),
stringsAsFactors = FALSE)
known_variants## chr pos gene
## 1 12 25358650 LYRM5
## 2 12 21788465 LDHB
## 3 12 21797029 LDHB
## 4 12 25398281 KRASThe minimum information needed are the chr and
pos columns; any additional columns (such as
gene, here) will just be passed along for later use. We can
now pass this set (along with our SNV profiles) to the
list_variants function:
## chr pos gene HCT116 RKO
## 1 12 21788465 LDHB G/T G/G
## 2 12 21797029 LDHB G/G G/G
## 3 12 25358650 LYRM5 A/T A/T
## 4 12 25398281 KRAS C/T 0While this gives you a nice little list of the genotypes of your
specified variants, we can also visualise this using the
plot_variant_list function. It takes a slightly modified
version of the output from the list_variants function: it
may only contain the genotype columns. We thus need to create row names
to identify the variants, like this:
# Set row names to "chr: pos (gene)"
row.names(variant_list) <- paste0(variant_list$chr, ":", variant_list$pos,
" (", variant_list$gene, ")")
# Remove "chr", "pos" and "gene" columns
to_remove <- c("chr", "pos", "gene")
variant_list <- variant_list[, !names(variant_list) %in% to_remove]
# Plot the genotypes in a grid
genotype_grid <- plot_variant_list(variant_list)## Warning: `gather_()` was deprecated in tidyr 1.2.0.
## ℹ Please use `gather()` instead.
## ℹ The deprecated feature was likely used in the seqCAT package.
## Please report the issue to the authors.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
## of ggplot2 3.3.4.
## ℹ The deprecated feature was likely used in the seqCAT package.
## Please report the issue to the authors.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
This gives us an easily overviewed image of what variants are present
in which samples, and their precise genotype. We can see that the
KRASG13D mutation is indeed present in the HCT116, but not in
RKO. We can also see that RKO has a homozygous G/G genotype
for one of the LDHB variants, while HCT116 is heterozygous
(T/G) for the same. (Please note that this data was
aligned and analysed using the GRCh37 / hg19 assembly and that listed
positions might not be accurate for other assemblies.)
Evaluating multiple comparisons
Many scientific studies compare more than just two datasets, not to
mention meta-studies and large-scale comparisons. It is therefore
important to be able to characterise and evaluate many-to-one or
many-to-many cases as well - the seqCAT package provides a
number of functions and procedures for doing so.
Performing multiple profile comparisons
The first step of such an analysis is to create and read SNV profiles
for each sample that is to be evaluated (please see section 2). The example data used
here has three different samples: HCT116, HKE3 and RKO. The
compare_many function is a helper function for creating
either one-to-many or many-to-many SNV profile comparisons, and returns
a list of the global similarities for all combinations of
profiles and their respective data (for downstream analyses):
# Create list of SNV profiles
profiles <- list(hct116, hke3, rko)
# Perform many-to-many comparisons
many <- compare_many(profiles)
many[[1]]## sample_1 sample_2 variants_1 variants_2 overlaps matches concordance
## 1 HCT116 HCT116 523 523 523 523 100.0
## 2 HCT116 HKE3 493 493 493 475 96.3
## 3 HCT116 RKO 259 259 259 181 69.9
## 4 HKE3 HKE3 1604 1604 1604 1604 100.0
## 5 HKE3 RKO 299 299 299 204 68.2
## 6 RKO RKO 583 583 583 583 100.0
## similarity_score
## 1 99.1
## 2 95.4
## 3 68.7
## 4 99.7
## 5 67.2
## 6 99.2We can here see the summary statistics of all three combinations of
the cell lines in the example data. Notice that
compare_many will only perform a comparison that has not
already been performed, i.e. it will not perform the RKO
vs. HCT116 comparison if it has already performed HCT116 vs. RKO. Also
notice that it does perform self-comparisons (i.e. HCT116 vs.
HCT116), which is useful for downstream visualisations.
The similarities are stored in the first element of the results
(many[[1]]), while the data for each comparison is stored
in the second (many[[2]]). The second element is itself
also a list, whose indices correspond to the row names of the similarity
object. If we, for example, are interested in the HKE3 self-comparison,
we can see that its row name is 4. We can then access its
data like this:
## chr pos sample_1 sample_2 match rsID gene ENSGID
## 1 12 73805 HKE3 HKE3 match rs375835195 RP11-598F7.1 ENSG00000249054
## 2 12 75190 HKE3 HKE3 match rs374099059 AC215219.1 ENSG00000238823
## 3 12 75308 HKE3 HKE3 match rs370314061 AC215219.1 ENSG00000238823
## 4 12 75337 HKE3 HKE3 match rs147539459 AC215219.1 ENSG00000238823
## 5 12 76316 HKE3 HKE3 match rs370768066 AC215219.1 ENSG00000238823
## 6 12 76349 HKE3 HKE3 match rs71412503 AC215219.1 ENSG00000238823
## ENSTID REF ALT impact effect feature biotype
## 1 ENST00000504074 G C MODIFIER downstream_gene_variant transcript lincRNA
## 2 ENST00000458783 A G MODIFIER upstream_gene_variant transcript miRNA
## 3 ENST00000458783 C T MODIFIER upstream_gene_variant transcript miRNA
## 4 ENST00000458783 A G MODIFIER upstream_gene_variant transcript miRNA
## 5 ENST00000458783 T C MODIFIER upstream_gene_variant transcript miRNA
## 6 ENST00000458783 A G MODIFIER upstream_gene_variant transcript miRNA
## DP.HKE3 AD1.HKE3 AD2.HKE3 A1.HKE3 A2.HKE3 FILTER.HKE3 warnings.HKE3
## 1 15 8 7 G C PASS
## 2 45 39 6 A G PASS
## 3 38 38 C C PASS
## 4 38 27 11 A G PASS
## 5 63 46 17 T C PASS
## 6 44 35 9 A G PASSYou may also specify the a and b similarity
score parameters, as above. If you are interested in only a one-to-many
comparison (for cases when you have a “true” baseline profile to compare
against), you can do this by also specifying the
one = <profile> parameter in the function call. This
is useful if you have a COSMIC profile to compare against, for
example:
## sample_1 sample_2 variants_1 variants_2 overlaps matches
## 1 COSMIC.HCT116 COSMIC.HCT116 1 1 1 1
## 2 COSMIC.HCT116 HCT116 1 1 1 1
## 3 COSMIC.HCT116 HKE3 1 1 1 1
## 4 COSMIC.HCT116 RKO 1 1 0 0
## concordance similarity_score
## 1 100 28.6
## 2 100 28.6
## 3 100 28.6
## 4 NaN 16.7It is important to note that performing many comparisons like this may take quite some time, depending on the number of profiles and how much data each profile has. By returning all the data in a list you may then save each comparison to a file, for later re-analysis without having to re-do the comparisons.
Visualising multiple comparisons
A useful and straightforward way of visualising multiple profile
comparisons is to use a heatmap. We can use the summary statistics
listed in the similarity object from above as input to the function
plot_heatmap, which gives you a simple overview of all your
comparisons:
Here we see a blue colour gradient for the similarity score of the
three cell lines, which are clustered according to their similarity
(using cluster = TRUE, as default). You may change the size
of the text annotations using annotation_size = 5 (default)
or suppress them entirely (annotate = FALSE). You may also
suppress the legend (legend = FALSE), change the main
colour of the gradient (colour = "#1954A6" by default) or
change the limits of the gradient
(limits = c(0, 50, 90, 100) by default). The choice of
gradient limits are based on clarity (comparisons with a similarity
score less than 50, i.e. those that likely have too few
overlapping variants to begin with, are suppressed) and the previously
mentioned 90 % concordance threshold (Yu et
al. 2015).
This heatmap makes it clear that HCT116 and HKE3 are, indeed, very similar to each other, while RKO differs from them both. These types of heatmaps can be created for an arbitrary number of samples, which will then give a great overview of the global similarities of all the samples studied. This can be used to evaluate the quality of the datasets (e.g. to see which comparisons have very few overlaps), find similarity clusters and potential unexpected outliers. If a sample stands out in a heatmap such as this, that is grounds for further investigation, using both the methods described above and more classical evaluations of sequencing data (read quality, adapter contamination, alignments, variant calling, and so on).
Citation
If you are using seqCAT to analyse your data, please cite the following article:
seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data
Fasterius E. and Al-Khalili Szigyarto C.
F1000Research (2018), 7:1466
https://f1000research.com/articles/7-1466
Session info
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] seqCAT_1.29.0 VariantAnnotation_1.52.0
## [3] Rsamtools_2.22.0 Biostrings_2.75.0
## [5] XVector_0.46.0 SummarizedExperiment_1.36.0
## [7] Biobase_2.67.0 MatrixGenerics_1.19.0
## [9] matrixStats_1.4.1 GenomicRanges_1.59.0
## [11] GenomeInfoDb_1.43.0 IRanges_2.41.0
## [13] S4Vectors_0.44.0 BiocGenerics_0.53.0
## [15] BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 farver_2.1.2 dplyr_1.1.4
## [4] blob_1.2.4 bitops_1.0-9 fastmap_1.2.0
## [7] RCurl_1.98-1.16 GenomicAlignments_1.43.0 XML_3.99-0.17
## [10] digest_0.6.37 lifecycle_1.0.4 KEGGREST_1.47.0
## [13] RSQLite_2.3.7 magrittr_2.0.3 compiler_4.4.1
## [16] rlang_1.1.4 sass_0.4.9 tools_4.4.1
## [19] utf8_1.2.4 yaml_2.3.10 rtracklayer_1.66.0
## [22] knitr_1.48 labeling_0.4.3 S4Arrays_1.6.0
## [25] bit_4.5.0 curl_5.2.3 DelayedArray_0.33.1
## [28] abind_1.4-8 BiocParallel_1.41.0 withr_3.0.2
## [31] purrr_1.0.2 sys_3.4.3 grid_4.4.1
## [34] fansi_1.0.6 colorspace_2.1-1 ggplot2_3.5.1
## [37] scales_1.3.0 cli_3.6.3 rmarkdown_2.28
## [40] crayon_1.5.3 generics_0.1.3 httr_1.4.7
## [43] rjson_0.2.23 DBI_1.2.3 cachem_1.1.0
## [46] zlibbioc_1.52.0 parallel_4.4.1 AnnotationDbi_1.69.0
## [49] BiocManager_1.30.25 restfulr_0.0.15 vctrs_0.6.5
## [52] Matrix_1.7-1 jsonlite_1.8.9 bit64_4.5.2
## [55] GenomicFeatures_1.59.0 maketools_1.3.1 jquerylib_0.1.4
## [58] tidyr_1.3.1 glue_1.8.0 codetools_0.2-20
## [61] gtable_0.3.6 BiocIO_1.17.0 UCSC.utils_1.2.0
## [64] munsell_0.5.1 tibble_3.2.1 pillar_1.9.0
## [67] htmltools_0.5.8.1 GenomeInfoDbData_1.2.13 BSgenome_1.75.0
## [70] R6_2.5.1 evaluate_1.0.1 lattice_0.22-6
## [73] highr_0.11 png_0.1-8 memoise_2.0.1
## [76] bslib_0.8.0 SparseArray_1.6.0 xfun_0.48
## [79] buildtools_1.0.0 pkgconfig_2.0.3