Multiple research projects have accumulated data on the frequency of single nucleotide polymorphisms (SNPs) between individuals. These datasets provide an important resource to analyze individual and population level variation if the individual SNPs can be accurately assigned to specific gene loci. We have taken advantage of this resource by utilizing two processes. First, we amalgamated the various SNP databases into a single searchable program based on the assignment of individual SNPs to the human GRCh37 and GRCh38 assemblies. Second, we utilized the ability to assign IGHV, IGHD and IGHJ sequences to defined genomic loci within the same assemblies, thereby confirming the individual SNP variant locations within verified IG gene variants.

The resultant program, termed IgSNPer, analyzes each nucleotide position within a complete variant allele, identifying whether specific nucleotide variations can be explained through the presence of a SNP variant within the amalgamated SNP databases above a particular frequency. IgSNPer uses dbSNP build 156 for humans, which contains 1,130,597,309 reference SNP (rs) calls in total. Of these, 33,714,196 are on chromosome 14, where the immunoglobulin heavy chain (IGH) genes are located. This accumulated SNP reference set includes data from various population databases, including:

1. dbGaP_PopFreq: Aggregated frequency data on over 1 million individuals.
2. 1000Genomes: Includes data for 2,504 individuals from a total of 26 populations.
3. GnomAD: A variant collection incorporating 602M SNVs and 105M indels identified through whole-genome sequencing of 71,702 samples that were subsequently mapped to the GRCh38 reference assembly.
4. ExAC: The Exome Aggregation Consortium (ExAC) dataset accumulated SNP variation data on 60,706 unrelated individuals that were sequenced during the analysis of several disease specific and population related projects.
5. TOPMED: The TOPMED dataset utilizes data from 158,000 individuals of mainly European, African, Hispanic/Latino or East Asian ancestry.
6. TOMMO: An allele frequency panel produced from the genomic sequence analysis of 8380 Japanese individuals.
7. KOREAN Reference Genome Database: containing SNP variation data on 1465 Korean individuals

The program examines each full-length allelic sequence, identifying both common SNP variants according to the amalgamated SNP database, and uncommon variations that are either present at low frequency within the database or are not present in previously published SNPs within the database (labeled as uncommon). Each individual uncommon variation identified is given an IgSNPer score of one. The full IgSNPer score for each allele sequence is the sum of all uncommon variant nucleotides for that sequence. The resultant IgSNPer output for each allele provides an indication of whether a single or multiple rare SNP variants are present in that allelic sequence, with a score of zero indicating that the specific variation is found above the cutoff frequency within the set of individuals of the amalgamated SNP database.

The IgSNPer output serves several purposes. First, allelic sequences with zero scores indicate that the variation has been reported to be present in the human population at a certain frequency. Second, verified alleles with low IgSNPer counts (usually 1) reveal variations that are present at low frequency in the set of individuals in the reference set, for example alleles that may be specific to a population group that has not been utilized in the reference dataset. Finally, high IgSNPer counts are indicative of sequences that have an accumulation of variations that are absent in the reference set. Extreme caution should be taken with such alleles as a high IgSNPer score indicates technical issues such as those associated with truncated or incomplete alleles, or sequence errors present in such sequences.

Currenly under construction, this section will be provided later.