Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants

. 2021 Apr 20;2(4):100250. doi: 10.1016/j.xcrm.2021.100250

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples

DNA from 86 Brugada syndrome patients	This paper	N/A

Chemicals and reagents

Supreme NZYLong DNA polymerase	NZYTech	MB331
dNTPs NZYMix	NZYTech	MB086
Pure IT ExoZap	Ampliqon	A620601
Agencourt AMPure XP Beads	Beckman Coulter	A63881
LongAmp Taq 2X Master Mix	NEB	M0287
Short read eliminator XS	Circulomics	SKU SS-100-121-01
NEBNext Companion Module for Oxford Nanopore Technologies Ligation Sequencing	NEB	E7180
NEBNext Quick Ligation Module	NEB	E6056

Critical commercial assays

Nextera Rapid Capture Custom Enrichment Kit	Illumina	FC-140-1008
PCR Barcoding Expansion Pack 1-96	Oxford Nanopore Technologies	EXP-PBC096
Oxford Nanopore 1D DNA ligation Sequencing Kit	Oxford Nanopore Technologies	SQK-LSK109
Flow Cell Priming Kit	Oxford Nanopore Technologies	EXP-FLP002

Deposited data

Raw and analyzed data	This paper	EGAS00001004927
Scripts	This paper	https://github.com/Mel-lina/Brugada
Script for CTCF-motif orientation analysis	This paper	https://github.com/bdolmo/DeepBindTK
ChIP-seq data for DHS from HCMs	Encode Project Consortium⁴³	GSM736516 and GSM736504
ChIP-seq data for H3K4me3 from HCMs	Thurman et al.⁴⁴	GSM945308
ChIP-seq data for CTCF from HCMs	Wang et al.⁴⁵	GSM1022657 and GSM1022677
Hi-C-seq data from hESCs	Dixon et al.⁴⁷	GSM862723 and GSM892306
WGS genotypes from Human subjects	Erikson et al.⁵⁵	RRID:SCR_011519
WGS genotypes from Human subjects	1000 Genomes Project Consortium et al.³⁹	RRID:SCR_006828
WGS genotypes from Human Subjects	GTEx Consortium et al.⁵⁶	RRID:SCR_013042
Illumina OMNI 2.5 genotypes from Human subjects	10000 Genome Project Consortium et al.³⁹	RRID:SCR_006828
WGS genotypes from Human subjects	Karczewski et al.⁵⁴	RRID:SCR_014964
RNA-Seq data from Human Heart Left Ventricle samples	GTEx Consortium et al.⁵⁶	RRID:SCR_013042
Phased genotypes from Human subjects	GTEx Consortium et al.⁵⁶	RRID:SCR_013042
Low complexity regions in the human genome GRCh37/hg19	Li⁸⁷	Li, 2014⁸⁷
GATK Bundle for human reference genome hg19	Broad Institute	gsapubftp-anonymous@ftp.broadinstitute.org

Oligonucleotides

Tailed forward primer for long-range PCR: TTCTGTTGGTGCTGATATTGCGCCATGACCA TTGTTATTTGTCCAGA	This paper	N/A
Tailed reverse primer for long-range PCR: ACTTGCCTGTCGCTCTATCTTCCCTGAAG AAATGTCACGGCTTGTTAG	This paper	N/A
Tailed forward primer for nested long-range PCR: TTCTGTTGGTGCTGATATTGCAGTAACTGAA AATGCTTCTGAGTGGC	This paper	N/A
Tailed reverse primer for nested long-range PCR: ACTTGCCTGTCGCTCTATCTTCTTGAAGAG AGGTGACAAAACAAAGGG	This paper	N/A

Software and algorithms

HOMER	Benner at al.¹¹	RRID:SCR_010881
DesignStudio™	Illumina	https://www.illumina.com/products/by-type/informatics-products/designstudio.html
Skewer v0.1.123	Jiang et al.⁸⁸	RRID:SCR_001151
BWA-MEM v0.7.17	Li and Durbin⁸⁹	RRID:SCR_010910
SAMtools v1.3.1	Li et al.⁹⁰	RRID:SCR_002105
Picard v2.18.9	Broad Institute	RRID:SCR_006525
GATK v3.8-0	Mckenna et al.⁵³	RRID:SCR_001876
PLINK v1.90b6.9	Purcell et al.⁹¹	RRID:SCR_001757
Rtsne	Van der Maaten and Hinton⁹²	RRID:SCR_016342
HaploView v4.2	Barrett et al.⁴⁰	RRID:SCR_003076
Beagle5.1	Browning et al.⁶⁰	RRID:SCR_001789
SHAPEIT4	Delaneau et al.⁶¹	https://odelaneau.github.io/shapeit4/
Guppy v3.2.10	Oxford Nanopore Technologies	https://nanoporetech.com/
minimap2 v2.17	Li⁹³	RRID:SCR_018550
WhatsHap v0.18	Patterson et al.⁶⁴	https://whatshap.readthedocs.io/en/latest/
R v3.5.2	R Project	https://www.r-project.org/
ggplot2	R Project	https://cran.r-project.org/web/packages/ggplot2/index.html
IGV	Broad Institute	RRID:SCR_011793
DESeq2	Love et al.⁶⁷	RRID:SCR_015687
MOFA+	Argelaguet et al.⁶⁷	https://biofam.github.io/MOFA2/

Other

MinION Flow Cell R9	Oxford Nanopore	FLO-MIN106D