findNovelAlleles

findNovelAlleles - Find novel alleles from repertoire sequencing data

Description¶

findNovelAlleles analyzes mutation patterns in sequences thought to align to each germline allele in order to determine which positions might be polymorphic.

Usage¶

findNovelAlleles(
data,
germline_db,
v_call = "v_call",
j_call = "j_call",
seq = "sequence_alignment",
junction = "junction",
junction_length = "junction_length",
germline_min = 200,
min_seqs = 50,
auto_mutrange = TRUE,
mut_range = 1:10,
pos_range = 1:312,
pos_range_max = NULL,
y_intercept = 0.125,
alpha = 0.05,
j_max = 0.15,
min_frac = 0.75,
nproc = 1
)

Arguments¶

data: data.frame containing repertoire data. See details.
germline_db: vector of named nucleotide germline sequences matching the V calls in data. These should be the gapped reference germlines used to make the V calls.
v_call: name of the column in data with V allele calls. Default is v_call.
j_call: name of the column in data with J allele calls. Default is j_call.
seq: name of the column in data with the aligned, IMGT-numbered, V(D)J nucleotide sequence. Default is sequence_alignment.
junction: Junction region nucleotide sequence, which includes the CDR3 and the two flanking conserved codons. Default is junction.
junction_length: Number of junction nucleotides in the junction sequence. Default is junction_length.
germline_min: the minimum number of sequences that must have a particular germline allele call for the allele to be analyzed.
min_seqs: minimum number of total sequences (within the desired mutational range and nucleotide range) required for the samples to be considered.
auto_mutrange: if TRUE, the algorithm will attempt to determine the appropriate mutation range automatically using the mutation count of the most common sequence assigned to each allele analyzed.
mut_range: range of mutations that samples may carry and be considered by the algorithm.
pos_range: range of IMGT-numbered positions that should be considered by the algorithm.
pos_range_max: Name of the column in data with the ending positions of the V alignment in the germline (usually v_germline_end). The end of the alignment will be used to limit the range of positions to be considered to count mutations. With NULL all positions in the IMGT V region will be considered. In this case, in sequences where the V was trimmed on the 3’, mutated nucleotides could include nucleotides from the CDR3.
y_intercept: y-intercept threshold above which positions should be considered potentially polymorphic.
alpha: alpha value used for determining whether the fit y-intercept is greater than the y_intercept threshold.
j_max: maximum fraction of sequences perfectly aligning to a potential novel allele that are allowed to utilize to a particular combination of junction length and J gene. The closer to 1, the less strict the filter for junction length and J gene diversity will be.
min_frac: minimum fraction of sequences that must have usable nucleotides in a given position for that position to considered.
nproc: number of processors to use.

Value¶

A data.frame with a row for each known allele analyzed. Besides metadata on the the parameters used in the search, each row will have either a note as to where the polymorphism-finding algorithm exited or a nucleotide sequence for the predicted novel allele, along with columns providing additional evidence.

The output contains the following columns:

germline_call: The input (uncorrected) V call.
note: Comments regarding the inferrence.
polymorphism_call: The novel allele call.
nt_substitutions: Mutations identified in the novel allele, relative to the reference germline (germline_call)
novel_imgt: The novel allele sequence.
novel_imgt_count: The number of times the sequence novel_imgt is found in the input data. Considers the subsequence of novel_imgt in the pos_range.
novel_imgt_unique_j: Number of distinct J calls associated to novel_imgt in the input data. Considers the subsequence of novel_imgt in the pos_range.
novel_imgt_unique_cdr3: Number of distinct CDR3 sequences associated with novel_imgt in the input data. Considers the subsequence of novel_imgt in the pos_range.
perfect_match_count: Final number of sequences retained to call the new allele. These are unique sequences that have V segments that perfectly match the predicted germline in the pos_range.
perfect_match_freq: perfect_match_count / germline_call_count
germline_call_count: The number of sequences with the germline_call in the input data that were initially considered for the analysis.
germline_call_freq: The fraction of sequences with the germline_call in the input data initially considered for the analysis.
germline_imgt: Germline sequence for germline_call.
germline_imgt_count: The number of times the germline_imgt sequence is found in the input data.
mut_min: Minimum mutation considered by the algorithm.
mut_max: Maximum mutation considered by the algorithm.
mut_pass_count: Number of sequences in the mutation range.
pos_min: First position of the sequence considered by the algorithm (IMGT numbering).
pos_max: Last position of the sequence considered by the algorithm (IMGT numbering).
y_intercept: The y-intercept above which positions were considered potentially polymorphic.
y_intercept_pass: Number of positions that pass the y_intercept threshold.
snp_pass: Number of sequences that pass the y_intercept threshold and are within the desired nucleotide range (min_seqs).
unmutated_count: Number of unmutated sequences.
unmutated_freq: Number of unmutated sequences over germline_imgt_count.
unmutated_snp_j_gene_length_count: Number of distinct combinations of SNP, J gene, and junction length.
snp_min_seqs_j_max_pass: Number of SNPs that pass both the min_seqs and j_max thresholds.
alpha: Significance threshold to be used when constructing the confidence interval for the y-intercept.
min_seqs: Input min_seqs. The minimum number of total sequences (within the desired mutational range and nucleotide range) required for the samples to be considered.
j_max: Input j_max. The maximum fraction of sequences perfectly aligning to a potential novel allele that are allowed to utilize to a particular combination of junction length and J gene.
min_frac: Input min_frac. The minimum fraction of sequences that must have usable nucleotides in a given position for that position to be considered.

The following comments can appear in the note column:

Novel allele found: A novel allele was detected.
Same as:: The same novel allele sequence has been identified multiple times. If this happens, the function will also throw the message ‘Duplicated polymorphism(s) found’.
Plurality sequence too rare: No sequence is frequent enough to pass the J test (j_max).
A J-junction combination is too prevalent: Not enough J diversity (j_max).
No positions pass y-intercept test: No positions above y_intercept.
Insufficient sequences in desired mutational range: mut_range and pos_range.
Not enough sequences: Not enough sequences in the desired mutational range and nucleotide range (min_seqs).
No unmutated versions of novel allele found: All observed variants of the allele are mutated.

Details¶

The TIgGER allele-finding algorithm, briefly, works as follows: Mutations are determined through comparison to the provided germline. Mutation frequency at each position is determined as a function of sequence-wide mutation counts. Polymorphic positions exhibit a high mutation frequency despite sequence-wide mutation count. False positive of potential novel alleles resulting from clonally-related sequences are guarded against by ensuring that sequences perfectly matching the potential novel allele utilize a wide range of combinations of J gene and junction length.

Examples¶

# Note: In this example, with SampleGermlineIGHV,
# which contains reference germlines retrieved on August 2014,
# TIgGER finds the allele IGHV1-8*02_G234T. This allele
# was added to IMGT as IGHV1-8*03 on March 28, 2018.

# Find novel alleles and return relevant data
novel <- findNovelAlleles(AIRRDb, SampleGermlineIGHV)
selectNovel(novel)

  germline_call                note polymorphism_call nt_substitutions
1    IGHV1-8*02 Novel allele found!  IGHV1-8*02_G234T           234G>T
                                                                                                                                                                                                                                                                                                                        novel_imgt
1 CAGGTGCAGCTGGTGCAGTCTGGGGCT...GAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTC............ACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAAC......AGTGGTAACACAGGCTATGCACAGAAGTTCCAG...GGCAGAGTCACCATTACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG
  novel_imgt_count novel_imgt_unique_j novel_imgt_unique_cdr3
1              657                   6                    626
  perfect_match_count perfect_match_freq germline_call_count germline_call_freq
1                 661          0.7295806                 906              0.052
  mut_min mut_max mut_pass_count
1       1      10            760
                                                                                                                                                                                                                                                                                                                     germline_imgt
1 CAGGTGCAGCTGGTGCAGTCTGGGGCT...GAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTC............ACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAAC......AGTGGTAACACAGGCTATGCACAGAAGTTCCAG...GGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG
  germline_imgt_count pos_min pos_max y_intercept y_intercept_pass snp_pass
1                   0       1     312       0.125                1      754
  unmutated_count unmutated_freq unmutated_snp_j_gene_length_count
1             661      0.7295806                                83
  snp_min_seqs_j_max_pass alpha min_seqs j_max min_frac
1                       1  0.05       50  0.15     0.75