1  Summary-level Quality Control

1.1 Overview

QC procedure for HERMES 2.0 GWAS meta-analysis for Heart Failure subtypes was performed using snakemake workflow management system designed to follow the procedure described in Winkler T, et al. 2014

The workflow was designed to process each input GWAS summary statistics file, grouped by study/cohort, phenotype, imputation reference panel, and ancestry.

The following diagram illustrates the rule graph (Figure 1.1 (a)) and file graph, i.e. rule graph with expected input and output file(s), (Figure 1.1 (b)) for a given input GWAS summary statistics.

(a) QC rule graph

(b) QC file graph

Figure 1.1: Schematic diagram of GWAS summary statistics quality control

In the above figure, each polygon represents a rule to perform a specific QC process. All upstream rules need to be completed in order to advance to the next one. This modularisation helps to identify potential issues in intermediate steps, and to minimise error in the final results.

1.1.1 Rule description

Rule(s)	Description
test_read	Test read the first 100 lines of a raw input GWAS summary statistics file to check for consistency with the requested format
raw_to_ready	Reformat a raw input GWAS summary statistics file (e.g. reorder & rename columns) for further QC processing
qc_step1	Step 1 QC: sanity check, create unique variant ID, harmonise allele (see Note )
qc_step2	Step 2 QC: QC based on allele comparison with reference panel (see Note ). For I/O efficiency, this step also makes an AFCHECK plot (allele frequency comparison with reference panel)
plot_qq	Make QQPLOT (observed vs. expected log P-value)
plot_pz	Make PZPLOT (reported vs. calculated P-value)
get_ref_1000G format_ref_1000G	Download and format reference variant file from The 1000 Genome project
format_ref_tabix	Format and create a tabix index for reference variant file
get_ref_HRC_EUR	For European ancestry, download reference genome from the Haplotype Reference Consortium (HRC)
concat_HRC_1000G_EUR	For European ancestry, take the union of reference variants from HRC and 1000G projects

Note {#sec-qc-note}

Step 1 QC

• For sanity check, the qc_step1 rule excludes variants with any of the following criteria:
  • beta > 10
  • standard error > 10
  • P value outside 0-1 range
  • imputation (INFO) score outside 0-1 range
  • Allele frequencies outside 0-1 range
  • N effective < 50
  • imputation (INFO) score < 0.6
  • If INFO score is missing & N effective cannot be calculated:
    • Minor allele frequency (MAF) < 0.01
• N effective (effective sample size) is calculated as $N_{eff}=2\times MAF\times (1-MAF)\times N_{total}\times INFO$
• Each variant will be assigned a unique ID in the format chr:pos:A1_A2, where chr:pos refers to chromosome and base pair position according to the NCBI GRCh37 genome assembly, and A1_A2 refers to allele 1 (effect allele) and allele 2 (other allele) in alphabetical order.
• Accordingly, the regression coefficient (i.e. beta / log odds) of each variant is harmonised to reflect the effect allele (A1)

Step 2 QC

• Based on allele comparison with reference panel, the qc_step2 rule further excludes variants with any of the following criteria:
  • unique variant ID not found in the reference panel (as the unique variant ID is constructed using genomic position and allele information, this will exclude any mismatch on those)
  • MAF difference with reference panel > 0.2

1.2 Abbreviation

1.2.1 Phenotype

Phenotype ID	Phenotype	Abbreviation	Description
Pheno1	Heart Failure	HF	Clinical syndrome of HF, any cause or manifestation
Pheno2	Non-ischaemic HF	ni-HF	HF excluding CAD, valvular or congenital HD
Pheno3	Non-ischaemic HFrEF	ni-HFrEF	HF excluding CAD, valvular or congenital HD; with left ventricular ejection fraction (LVEF) < 50%
Pheno4	Non-ischaemic HFpEF	ni-HFpEF	HF excluding CAD, valvular or congenital HD; with LVEF ≥50%

1.2.2 Ancestry

Ancestry ID	Description
EUR	European
AFR	African
EAS	East Asian
SAS	South Asian
HSP	Hispanic (Admixed American)

1.3 Reference panel

To check for allele mismatch and allele frequency in Step 2 QC, input GWAS summary statistics were compared against population-specific reference panels from 1000G Phase 3 downloaded from McCarthy Group Tools which has variant-level allele information on 85,167,453 genetic variants. To maximise variants coverage for European (EUR) population, a custom reference panel was used by taking the union of variants from 1000G Phase 3 and 39,131,578 autosomal polymorphic SNPs reference panel estimated from 32,470 samples from HRC v1.1 sites information. In case of overlap, the allele information from HRC panel was used.

The non-duplicated union of the 1000G and HRC panel for EUR population covers 94,108,954 variants in total. For efficiency, rare variants with MAF < 0.001 were removed from the European reference panel, leaving a total of 56,651,511 reference variants for QC.

1.4 QC summary

The current QC pipeline processed a total of 99 individual GWAS summary statistics.

QC for summary statistics from BIOSTAT-CHF, COGEN, PREVEND, LURIC, GRADE, RS1, WGHS for all-cause HF (European ancestry)

followed the procedure described in Shah S, Henry A, et al. (2020) as there were no further data update.

1.4.1 Variant QC

Figure 1.2: Number of variants per GWAS summary statistics

Table 1.1: Summary of variant QC per phenotype

		N variant
	N study	min	max	median	IQR
Heart failure
pre QC	42	4,249,509	61,345,317	10,971,762	11,474,057
post QC step 1	42	1,935,063	20,565,290	7,923,824	2,295,228
post QC step 2	42	1,918,443	14,136,875	7,818,278	2,340,751
Non-ischaemic HF
pre QC	31	4,249,509	61,345,317	14,516,442	11,318,293
post QC step 1	31	1,904,407	19,347,458	7,590,322	2,498,026
post QC step 2	31	1,888,150	13,189,394	7,534,196	2,342,188
Non-ischaemic HFrEF
pre QC	15	1,521,114	39,127,678	11,989,532	14,818,308
post QC step 1	15	1,214,205	20,329,184	7,474,255	5,005,720
post QC step 2	15	1,168,715	13,688,124	7,474,109	4,775,980
Non-ischaemic HFpEF
pre QC	11	4,249,509	35,857,117	9,770,432	10,530,544
post QC step 1	11	4,231,482	12,501,421	7,557,557	2,694,924
post QC step 2	11	4,209,933	11,924,532	7,524,239	2,729,505

1.4.2 Genomic Inflation

Figure 1.3: Genomic inflation coefficient (${\lambda }_{GC}$) across phenotypes

1.4.3 Study-specific QC

The following section describes QC results organised by study (in alphabetical order) and ancestry groups

ARIC (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	27,996,260	9,105,497	9,105,442
Non-ischaemic HF	0.99	26,736,821	8,730,892	8,730,848

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

ARIC (AFR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	0.99	61,345,317	14,248,446	14,136,875
Non-ischaemic HF	0.98	61,345,317	13,291,844	13,189,394

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

BBJ (EAS)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.06	8,678,731	8,643,865	8,641,438

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

BioSHiFT-TRIUMPH (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	0.97	15,107,891	7,614,815	7,614,106
Non-ischaemic HF	0.96	14,516,442	7,455,405	7,454,690
Non-ischaemic HFrEF	0.97	14,439,396	7,420,459	7,419,741

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

BioVU (AFR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	4,249,509	4,233,754	4,212,122
Non-ischaemic HF	0.99	4,249,509	4,233,101	4,211,500
Non-ischaemic HFrEF	0.86	4,249,509	4,231,365	4,209,817
Non-ischaemic HFpEF	0.85	4,249,509	4,231,482	4,209,933

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

BioVU (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	4,249,509	4,233,758	4,233,384
Non-ischaemic HF	1.01	4,249,509	4,233,758	4,233,384
Non-ischaemic HFrEF	1.00	4,249,509	4,233,758	4,233,384
Non-ischaemic HFpEF	1.00	4,249,509	4,233,758	4,233,384

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

CHS (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.03	8,412,100	7,641,670	7,641,519
Non-ischaemic HF	1.02	8,408,071	7,534,342	7,534,196
Non-ischaemic HFrEF	1.00	8,230,928	7,474,255	7,474,109
Non-ischaemic HFpEF	1.01	8,360,984	7,524,385	7,524,239

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

CHS (AFR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.03	18,623,911	9,515,374	9,399,474
Non-ischaemic HF	1.04	18,318,251	8,970,258	8,862,098

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

Chb (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.11	9,406,294	8,993,959	7,912,901
Non-ischaemic HF	1.04	9,406,294	8,995,473	7,913,053

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

DiscovEHR-GSA (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.06	36,078,228	12,839,176	12,148,073
Non-ischaemic HF	1.05	35,880,638	12,535,315	11,933,614
Non-ischaemic HFrEF	1.08	35,854,117	12,493,279	11,904,221
Non-ischaemic HFpEF	1.09	35,857,117	12,501,421	11,909,696

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

DiscovEHR-OMNI (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.05	35,822,503	13,131,366	12,479,687
Non-ischaemic HF	1.05	35,250,627	12,408,253	11,976,324
Non-ischaemic HFrEF	1.04	35,185,987	12,318,208	11,914,289
Non-ischaemic HFpEF	1.04	35,188,306	12,333,728	11,924,532

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

ELGH (SAS)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.00	9,527,863	6,974,723	6,934,779
Non-ischaemic HF	1.02	9,527,863	6,959,785	6,921,269

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

ENGAGE (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	11,235,578	10,544,441	10,385,394

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

EPHESUS (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.16	16,304,833	7,122,383	5,715,183

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

EPIC-Norfolk (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.02	18,718,562	10,734,847	10,691,251
Non-ischaemic HF	1.02	17,483,817	10,521,914	10,498,325

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

Estonian Biobank (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	0.99	26,977,518	20,565,290	13,734,905
Non-ischaemic HF	0.99	24,595,290	19,347,458	12,950,362
Non-ischaemic HFrEF	0.76	26,971,494	20,329,184	13,688,124

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

FHS (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.05	10,707,947	6,151,206	6,151,169
Non-ischaemic HF	1.04	10,093,810	5,985,569	5,985,534

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

FINNGEN-r3 (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.07	16,306,055	8,783,879	8,560,509

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

FOURIER (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	0.99	9,447,756	9,388,479	9,281,791

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

MHI Biobank (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	7,393,919	7,047,089	6,949,073

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

GoDARTS-AFFY (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	21,002,749	8,188,690	8,188,392
Non-ischaemic HF	1.01	19,548,958	7,750,515	7,750,320
Non-ischaemic HFrEF	1.01	19,324,337	7,669,575	7,669,401
Non-ischaemic HFpEF	1.01	19,231,613	7,649,551	7,649,392

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

GoDARTS-BROAD (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.02	16,187,471	6,792,628	6,792,627

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

GoDARTS-ILLUMINA (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.03	20,468,416	8,079,695	8,079,532
Non-ischaemic HF	1.03	19,172,863	7,714,258	7,714,138

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

HFH-Ipaad (AFR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.02	20,185,596	4,066,114	3,875,374
Non-ischaemic HF	1.03	19,155,995	3,523,211	3,338,179
Non-ischaemic HFrEF	1.03	18,560,116	3,210,609	3,026,858

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

HFH-Ipaad (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.06	15,506,822	6,396,996	6,396,991
Non-ischaemic HF	1.05	12,934,101	5,584,908	5,584,903
Non-ischaemic HFrEF	1.05	11,989,532	4,572,897	4,572,896

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

MAGnet (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.31	39,127,678	8,792,674	8,788,981
Non-ischaemic HF	1.21	39,127,678	8,160,891	8,160,553
Non-ischaemic HFrEF	1.20	39,127,678	8,114,471	8,114,205

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

MDCS (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	6,489,141	6,485,592	6,485,498
Non-ischaemic HF	1.01	6,489,361	6,484,622	6,484,532

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

MGB (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.04	6,339,358	6,286,124	6,279,005

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

ORIGIN (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.03	14,577,158	7,412,177	7,306,794
Non-ischaemic HF	1.00	14,554,754	7,163,152	7,062,252

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

ORIGIN (HSP)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.00	19,433,848	7,851,681	7,723,654
Non-ischaemic HF	0.99	19,414,242	7,590,322	7,467,225
Non-ischaemic HFpEF	1.00	19,412,629	7,557,557	7,435,025

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

PEGASUS (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	9,055,720	9,033,153	8,939,046

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

PIVUS (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	9,995,388	6,792,034	6,549,341
Non-ischaemic HF	1.01	9,906,601	6,661,738	6,424,135
Non-ischaemic HFrEF	1.34	1,521,114	1,214,205	1,168,715
Non-ischaemic HFpEF	1.02	9,770,432	6,617,054	6,381,122

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

PROSPER (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	21,716,400	8,432,519	8,432,215
Non-ischaemic HF	1.01	21,716,092	8,177,403	8,177,259

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

SAVOR (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	8,010,730	7,995,966	7,918,320

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

SHIP (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.02	24,339,579	6,693,612	6,692,979
Non-ischaemic HF	1.01	24,339,579	6,485,057	6,484,436

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

SOLID (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1	8,471,892	8,392,379	8,306,237

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

TwinGene (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.01	7,877,068	7,616,477	7,616,379
Non-ischaemic HF	1.02	7,877,068	7,616,473	7,616,374

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

UK Biobank (AFR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Non-ischaemic HF	0.94	5,194,188	3,906,050	3,885,934
Heart failure	1.00	5,194,188	3,997,379	3,976,808

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

UK Biobank (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.08	9,696,744	9,595,926	9,471,372
Non-ischaemic HF	1.05	9,696,744	9,595,926	9,471,372
Non-ischaemic HFrEF	1.02	9,696,744	9,595,926	9,471,372
Non-ischaemic HFpEF	0.56	9,696,744	9,595,926	9,471,372

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

UK Biobank (SAS)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.00	4,626,782	1,935,063	1,918,443
Non-ischaemic HF	0.92	4,626,782	1,904,407	1,888,150

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

ULSAM (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.02	10,148,359	7,197,917	6,887,633
Non-ischaemic HF	1.00	10,143,702	7,043,003	6,738,507
Non-ischaemic HFrEF	0.93	8,428,288	6,395,462	6,111,344
Non-ischaemic HFpEF	1.02	9,909,117	6,811,195	6,518,109

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT

 

deCODE (EUR)

		N variant
	${\lambda }_{GC}$	pre QC	post QC step 1	post QC step 2
Heart failure	1.02	9,222,170	9,222,170	8,886,869
Non-ischaemic HF	1.00	9,222,170	9,222,170	8,886,869
Non-ischaemic HFrEF	1.01	9,222,170	9,222,170	8,886,869
Non-ischaemic HFpEF	1.00	9,222,170	9,222,170	8,886,869

Plot	Heart failure	Non-ischaemic HF	Non-ischaemic HFrEF	Non-ischaemic HFpEF
AFCHECK
QQPLOT
PZPLOT