@inbook{bc885b3539554f3aa38f8e747af0106b,
title = "Accurate assembly and typing of HLA using a graph-guided assembler kourami",
abstract = "Accurate typing of human leukocyte antigen (HLA) is essential for successful organ transplantation and HLA genes are heavily associated with various diseases. Widely used typing assays often involve a set of specially designed primers or probes requiring additional experiments. With the maturing of high-throughput sequencing (HTS) technologies, whole genome sequencing (WGS) as well as other HTS assays are becoming more accessible even in the clinical settings. We describe various computational methods capable of directly typing HLA genes using HTS data including Kourami, our HLA assembler. Kourami is the first HLA assembler capable of discovering novel alleles. Kourami assembles full-length sequences across the peptide-binding regions of HLA genes. Here, we focus on how a user would use Kourami on a new sample. We demonstrate the application by typing HLA alleles from a recently published WGS data with validated HLA types using Kourami.",
keywords = "Assembly, Bioinformatics in silico, HLA, High-throughput, WGS, Whole genome sequencing",
author = "Heewook Lee and Carl Kingsford",
note = "Funding Information: 4. Largely due to the cost benefit, WES is extremely popular. Kourami can assemble HLA allele using WES data, although it was developed to work with WGS data. Based on the previous testing on HapMap WES data [8], typing accuracy is slightly lower (94.7%) when compared to WGS typing accuracy (>99%). A caution must be used when using WES as Kourami may skip HLA genes if there is no coverage in parts of the typ-ing exons. Known biases in WES such as reference allele bias, GC bias and coverage fluctuations [15, 16] may also have an effect on typing performance.FundingThis research was funded in part by the Gordon and Betty Moore Foundation{\textquoteright}s Data-Driven Discovery Initiative through Grant GBMF4554 to C.K., by the US National Science Foundation (CCF-1256087, CCF-1319998) and by the US National Institute of Health (R01HG007104, R01GM122935). Publisher Copyright: {\textcopyright} Springer Science+Business Media, LLC, part of Springer Nature 2018.",
year = "2018",
doi = "10.1007/978-1-4939-8546-3_17",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "235--247",
booktitle = "Methods in Molecular Biology",
}