Decoding the diversity of killer immunoglobulin-like receptors by deep sequencing and a high-resolution imputation method

. 2022 Mar 9;2(3):100101. doi: 10.1016/j.xgen.2022.100101

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples

The genotype data of BioBank Japan used in this study	Nagai et al. 2017³⁹	Japanese Genotype-phenotype Archive (JGA) with accession code JGAS000114/JGAD000123 and JGAS000114/JGAD000220 which can be accessed through application at https://humandbs.biosciencedbc.jp/en/hum0014-latest

Deposited data

Individual-level KIR alleles and KIR imputation reference panel used in this study	This paper	the National Bioscience Database Center (NBDC) Human Database (https://humandbs.biosciencedbc.jp/en/) with the accession code hum0114
Human reference genome NCBI build 37, GRCh37	Genome Reference Consortium	http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
IPD-KIR	The KIR Nomenclature committee	https://www.ebi.ac.uk/ipd/kir/

Experimental models: Cell lines

A cell line used for genotyping and constructing KIR reference in the Japanese population	the Japan Biological Informatics Consortium (JBIC)	https://bioresource.nibiohn.go.jp/psc/index.html
ECACC HLA typed collection	The International Histocompatibility Working Group (IHWG)	https://www.phe-culturecollections.org.uk/products/celllines/hlatyped/search.jsp

Software and algorithms

KIR genotyping algorithm	This paper	https://github.com/saorisakaue/KIR_project https://doi.org/10.5281/zenodo.5908796
BWA	Li et al. 2009⁴⁰	http://bio-bwa.sourceforge.net
KernelDensity module	scikit-learn of python	https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KernelDensity.html
GATK	Van der Auwera & O'Connor. 2020⁴¹	https://software.broadinstitute.org/gatk/
DeepVariant	Poplin et al. 2018²⁰	https://github.com/google/deepvariant
blast	Altschul et al. 1990⁴²	https://blast.ncbi.nlm.nih.gov/Blast.cgi
plink	Purcell et al. 2007⁴³	https://www.cog-genomics.org/plink/
eLD software	Okada 2018²⁴	http://www.sg.med.osaka-u.ac.jp/tools.html
multicoreTSNE	python package	https://github.com/DmitryUlyanov/Multicore-TSNE
Disentangler software	Okada et al. 2011⁴⁴	http://kumasakanatsuhiko.jp/projects/disentangler/
Beagle	Browning and Browning. 2007⁴⁵	https://faculty.washington.edu/browning/beagle/beagle.html
Minimac3	Das et al. 2016⁴⁶	https://genome.sph.umich.edu/wiki/Minimac3