DOI: 10.5061/dryad.cjsxksnjh
title: Unraveling the genetics of feline hypertrophic cardiomyopathy: A multiomics study of 138 cats

description: Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac
 disease in cats, often leading to congestive heart failure, arterial
 thromboembolism, and sudden cardiac death. The genetics of feline HCM are
 poorly understood, and limited genetic discoveries remain breed or
 family-specific. We aimed to identify novel causative or disease-modifying
 variants in a large cohort of cats reflective of the general cat
 population. In a second cohort, we sought to characterize transcriptomic
 differences between HCM-affected cats and healthy controls. DNA was
 isolated from 138 domestic cats (109 HCM and 29 controls). No single or
 combination of variants of high, moderate, or modifying impact were
 identified in genome-wide analysis to cause or modify the disease severity
 of HCM. Several rare high and moderate-impact variants in genes associated
 with human HCM were detected in diseased cats. In a second cohort, left
 ventricular (LV), interventricular septal (IVS), and left atrial (LA)
 tissues of 27 HCM-affected and 15 control cats were submitted for stranded
 mature RNA-sequencing at 50 million reads/sample. A total of 74, 115, and
 45 DEGs were upregulated and 8, 53, and 48 DEGs were downregulated in
 LVPW, IVS, and LA tissue, respectively, in HCM-affected cats compared to
 controls. Similar to humans, the genetic etiology of feline HCM remains
 unknown in a high proportion of cases. Transcriptomics revealed molecular
 signatures that may help identify novel HCM biomarkers or drug targets in
 future investigations.
description: <strong>WGS data generation</strong>
 A total of 1-2 mL of whole blood were collected from the
 cephalic, saphenous, or jugular vein into EDTA blood collection tubes. DNA
 was either isolated from whole blood or from buffy coats after whole blood
 centrifugation at 2000 rpm for 15 minutes. Genomic DNA isolation was
 performed using commercially available kits (Gentra Puregene Blood kit,
 QIAGEN, Hilden Germany; ArchivePure;5Prime) and by following the
 respective manufacturer’s protocol. High-quality unfragmented DNA was
 selected by a combination of 1% agarose gel visualization and
 spectrophotometric confirmation (a 260/280 ratio of ~1.8 and a
 concentration of &gt; 50 ng/uL; NanoDrop One/One, Thermofisher,
 Waltham, GA, USA). Samples were stored at -20°C until ready for shipment
 to Theragen Bio Co., Ltd, Gyeonggi-do, Republic of Korea for WGS.
 Paired-end DNA libraries were generated with a TruSeq DNA Nano library
 prep kit. Samples were then pooled and sequenced at ~30x coverage on the
 Illumina NovaSeq6000 platform. Paired-end read lengths were either 125bp
 or 150 bp. <strong>RNASeq data
 generation</strong> Tissues from the LA, IVS and
 LVPW were extracted and either flash frozen in liquid nitrogen or placed
 in RNA later within 30 minutes post-mortem. All samples were subsequently
 stored at -80°C until ready for shipment for RNA-Seq. All tissue samples
 available were sent to Azenta, South Plainfield, NJ for RNA-Seq. Total RNA
 was extracted from frozen cell samples using Qiagen RNeasy Plus Universal
 mini kit and following the manufacturer’s instructions (Qiagen, Hilden
 Germany). The polyA method was used to select for mature mRNA and samples
 subsequently underwent quality control. RNA samples were quantified using
 Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA). RNA
 integrity was evaluated using Agilent TapeStation 4200 (Agilent
 Technologies, Palo Alto, CA, USA). Only samples with an RNA Integrity
 Number (RIN) of &gt;7 were converted to cDNA and processed for
 stranded library prep. Paired-end 150 bp cDNA libraries were sequenced on
 the Illumina HiSeq platform at a read depth of ~50 million reads per
 sample.
description: # Unraveling the genetics of feline hypertrophic cardiomyopathy: A
 multiomics study of 138 cats Dataset DOI:
 [10.5061/dryad.cjsxksnjh](10.5061/dryad.cjsxksnjh) ## Description of the
 data and file structure ### Data available 1\. A population level vcf of
 polymorphic SNP and indel variants were called among 138 domestic cats
 with and without hypertrophic cardiomyopathy (HCM). The VCF was generated
 by mapping paired wgs fastq reads to the Fca126 reference genome with bwa
 mem and calling variants through GATK4 best practices. Variant annotations
 were generated with Ensembl's VEP based on Fca126 gene and exon
 boundaries.  The vcf file contains meta-information lines, followed by a
 header line specifying fixed fields per sample and subsequent data lines
 detail variants at genomic positions. The fixed fields include chromosome
 (CHROM), position (POS), identifier (ID), the reference base(s) (REF),
 alternate base(s) (ALT), quality (QUAL), filter status (FILTER), and
 additional information (INFO). Genotypes are encoded as allele values
 separated by ‘/’. The tabix is also included.  NCBI BioSample names are
 used as sample identifiers in the vcf. Metadata, including age, sex,
 breed, and HCM phenotype for each individual sample is included in the
 supplemental material of the accompanying manuscript. 2\. An RNASeq read
 count matrix generated from the RNA extracted from the left ventricle
 posterior wall (LVPW), left atrium (LA), and/or interventricular septum
 (IVS) of cats with and without hypertrophic cardiomyopathy. The read count
 matrix was generated by mapping paired RNASeq reads to the Fca126
 reference genome with STAR and counting reads with htseq. The column
 header of the matrix is the sample names and rows names are gene
 names. Read counts from every sample in the study is include. Sample Ids
 are in a BioSample-tissue-phenotype format, where tissue = LVPW, LA, IVS
 and phenotype =  A; affected or C; control. Metadata for each sample
 including age, sex, breed, and HCM phenotype is available in the
 supplemental material of the accompanying manuscript. ## **Files and
 variables** **File: hcm_cat_RNA_read_counts.csv** **Description:** RNASeq
 read counts from the LA, IVS and LVPW samples. Rows: Represent different
 genes (e.g., LOC102899061, TRNAE-UUC, CCDC115). Columns: Represent samples
 from different tissues or regions, associated with the sample IDs (e.g.,
 SAMN45893915_IVS-A) Additional Variables: * Gene symbol is defined by the
 Fcat126 gtf, available from NCBI.  **File: hcm_cat_sra.vcf.gz**
 **Description:** WGS population vcf file with BioSample names **File:
 hcm_cat_sra.vcf.gz.tbi** **Description:** tabix index file to assist
 searchability of the parent vcf with bcftools and other tools.