Description and first insights on a large genomic biobank of lung transplantation

Abstract

The main limitation to long-term lung transplant (LT) survival is chronic lung allograft dysfunction (CLAD), which leads to irreversible lung damage and significant mortality. Individual factors can impact CLAD, but no large genetic investigation has been conducted to date. We established the multicentric Genetic COhort in Lung Transplantation (GenCOLT) biobank from a rich and homogeneous sub-part of COLT cohort. GenCOLT collected DNA, high-quality GWAS (genome-wide association study) genotyping and robust HLA data for donors and recipients to supplement COLT clinical data. GenCOLT closely mirrors the global COLT cohort without significant variations in variables like demographics, initial disease and survival rates (P > 0.05). The GenCOLT donors were 45 years-old on average, 44% women, and primarily died of stroke (54%). The recipients were 48 years-old at transplantation on average, 45% women, and the main underlying disease was chronic obstructive pulmonary disease (45%). The mean follow-up time was 67 months and survival at 5 years was 57.3% for the CLAD subgroup and 97.4% for the non-CLAD subgroup. After stringent quality controls, GenCOLT gathered more than 7.3 million SNP and HLA genotypes for 387 LT pairs, including 91% pairs composed of donor and recipient of European ancestry. Overall, GenCOLT is an accurate snapshot of LT clinical practice in France and Belgium between 2009 and 2018. It currently represents one of the largest genetic biobanks dedicated to LT with data available simultaneously for donors and recipients. This unique cohort will empower to run comprehensive GWAS investigations of CLAD and other LT outcomes.

Fig. 1. Building the GenCOLT biobank and robust GWAS SNP data.

A Establishment of the GenCOLT DNA cohort. Initially, a total of 784 individuals were selected from the COLT biobank for DNA extraction and GWAS genotyping. After the initial screening, five individuals were excluded due to missing or deteriorated DNA sample. Subsequently, during the Axiom quality control procedure, four individuals were excluded due to failed experiments. Finally, a total of 387 pairs (n = 775 individuals), with DNA sample, accurate genomic and clinical data were included in the GenCOLT biobank. B Steps for GWAS genotyping data cleaning. The Axiom PMRA chip used for GWAS genotyping covers 902,560 SNPs. According to the manufacturer guidelines, 852,344 SNPs passed the primary technological quality controls. Upstream SNP imputation, we excluded SNPs with high level of missingness (>2%), with low frequency (<1%) and not respecting the HWE (p < 10^-6). Overall, GenCOLT contains 7.3 million high-quality SNP genotypes (DR or r² > 0.8) for 387 LT pairs. N.B. R, recipient; D, donor; GWAS, genome-wide association study; QC, quality control; SNP, single nucleotide polymorphism; MAF, minor allele frequency; HWE, Hardy-Weinberg equilibrium.

Fig. 2. Kaplan–Meier lung graft survival curves according to the rejection phenotypes vs. the non-CLAD grafts in GenCOLT.

The ‘CLAD’ subgroup includes the 4 ISHLT consensus phenotypes: BOS, RAS, mixed, and undefined. The ‘other’ subgroup refers to other types of primary rejection, including infectious-induced rejection and azithromycin-responsive allograft dysfunction (ARAD) in the first month’s post-surgery. N.B. BOS, bronchiolitis obliterans syndrome; RAS, restrictive allograft syndrome; ARAD, Azithromycin reversible allograft dysfunction; ISHLT, International Society for Heart and Lung Transplantation.

Fig. 3. Kaplan–Meier lung graft curves according to the CLAD vs. non-CLAD phenotypes for COLT and GenCOLT.

The ‘CLAD’ subgroup includes the 4 ISHLT consensus phenotypes: BOS, RAS, mixed, and undefined. N.B. BOS, bronchiolitis obliterans syndrome; RAS, restrictive allograft syndrome.

Fig. 4. Projection of GenCOLT individuals alongside the 1000 Genomes Project reference individuals.

A GenCOLT recipients and B GenCOLT donors. Using the GWAS SNP data, we projected GenCOLT individuals (represented by triangle) with the 1000 Genomes Project individuals (represented by circles) from five large reference populations. The triangle color refers to the percent of European ancestry for GenCOLT individuals as defined with ADMIXTURE (with darker shades indicating higher European ancestry). PCA principal component analysis, AFR African, AMR American, EAS East Asian, EUR European, SAS South Asian.