Shishi Luo (Song), Jane Yu, Yun Song
Genotyping Copy Number Variation in the Immunoglobulin Heavy Chain
Locus
The study of genomic regions that contain gene copies and structural variation
remains a major challenge in modern genomics. One such region is the
immunoglobulin heavy chain locus, which despite being an integral part of the
immune system, has only been completely sequenced twice. The locus contains
about 40 gene segments and varies in gene copy number and DNA sequence
between individuals. It would be useful to have a quantitative understanding of
this variation, given its potential implications for disease susceptibility. I will
introduce a method to extract the gene copy number of immunoglobulin genes
from whole genome sequencing (WGS) reads. Unlike other approaches that rely
on tailored sequencing experiments, this method leverages the increasing
availability of WGS datasets. The method performs well on simulated data.
Applying it to a small empirical dataset, we found patterns of variation in this
locus that were previously not known.