Introduction
Chronic kidney disease (CKD) affects over 850 million adults worldwide and is projected to be the 5th most common cause of years of life lost by 2040. CKD is defined by low estimated glomerular filtration rate (eGFR) and/or increased urine albumin to creatinine ratio (UACR). Genome wide association studies (GWAS) have reported associations of eGFR and UACR with thousands of common and low-frequency variants, but these variants account for only a small fraction of heritability. Rare variants (RVs) may account for some of the unaccounted heritability. Large-scale whole-genome sequencing (WGS) studies, such as the multi-ethnic NHLBI Trans-Omics Precision Medicine (TOPMed) Program, provide the opportunity to assess associations of eGFR and UACR with rare variants across the genome, especially in the noncoding region.

Hypothesis
Rare variant aggregations are associated with eGFR and UACR.

Methods
We applied our newly developed STAARpipeline to detect rare variants (MAF ≤ 0.01) associated with eGFR and UACR using 45,090 and 18,869 individuals from TOPMed Freeze 8 WGS data. STAARpipeline provides gene-centric analysis and non-gene-centric analysis using a variety of coding and noncoding masks. The gene-centric analysis provides five coding and eight noncoding functional categories. The non-gene-centric analysis includes sliding window analysis with fixed sizes and dynamic window analysis with data-adaptive sizes.

Results
For eGFR, the gene-centric analysis identified a genome-wide significant association of missense RVs in SLC47A1 at the Bonferroni-corrected level 5.00E-07 (=0.05/20,000/5). After conditioning on known eGFR-associated variants, the strength of the association was attenuated but it remained significant at level 2.50E-06. For UACR, the 2-kb sliding window procedure identified a genome-wide significant association of RVs in an intergenic region near ASB1 at the Bonferroni-corrected level 1.88E-08 (=0.05/2.66E06). After conditioning on known UACR-associated variants, the association remained significant at the same level 1.88E-08. The dynamic window procedure additionally detected two significant associations at the genome-wide error rate 0.05 level, including intronic RVs of TRIM67 and ERCC6L2. These two associations remained significant at level 1.88E-08 in conditional analysis.

Conclusions
Four new RV associations, including missense RVs in SLC47A1 with eGFR, RVs in an intergenic region near ASB1 with UACR, and intronic RVs of TRIM67 and ERCC6L2 with UACR, were identified using the TOPMed WGS Freeze 8 data through STAARpipeline. These findings suggest a role of rare variants in kidney traits.

Key Words:
Genome sequencing; Genome-wide association; Rare variants; Statistical Genetics; Complex Traits