Background/Purpose:  The antiphospholipid syndrome (APS) is an autoimmune disease characterized by the presence of antiphospholipid antibodies in serum together with clinical manifestations such as thrombosis, fetal loss, hemolytic anemia, and thrombocytopenia. Along with a crucial role of antiphospholipid antibody, proofs of the genetic predisposition of APS are not fully elucidated. The purpose of this study is to identify the novel genetic variations of primary and secondary Korean APS patient group.

Methods:  Genomic DNA was isolated from 6 patients of established APS and 6 age/gender-matched healthy control’s blood sample and whole-exome sequencing was performed using the Illumina HiSeq-2500 platform. Samples were submitted through analysis software where sequencing reads were mapped to the human reference genome (GRCh37, UCSC hg19 from NCBI, Feb 2009) using the Burrows-Wheeler Aligner algorithm, with removal of PCR duplicates using Picard. Local re-alignment, base quality recalibration and variant calling were performed using the Genome Analysis Toolkit. The potential effect of rare coding-sequence single nucleotide variants were predicted using predictive tools that included Polyphen-2, SIFT, and combined annotation-dependent depletion (CADD) Phred. To sort novel variation in patients group, <span”>all variants observed in HapMap, dbSNP, 1000 Genome, and NHLBI ESP6500 databases w<span”>ere filtered to be eliminated. Demographic, Clincal (cerebral infarction, pulmonary thromboembolism or recurrent pregnancy loss) and laboratory (lupus anticoagulant, anti-cardiolipin antibody, anti-beta2-glycoprotein1antibody) parameters were reviewed from the medical record of APS group.

Results:  Overall mean target exon coverage was 96.4% of targets with at least one read at a mean depth of 185–223× in patients group. A total of 43 potentially disease-associated variants observed in APS group that were absent from the reference databases were identified. 30 of them were missense variants (MST1L, TUBA3E, IDUA, HGC6.3, C7ORF26, MUC3A, METTL2B, RP1L1, ADAMTSL2, SUFU, TPBGL, CCDC168 etc), 11 frameshift (HLA-DR5, CD36, ATXN3, HS3ST6, LILRB3, FAM47C etc), and 2 stop variants (PABPC3, CCDC154). Notably, CD36gene on chromosome 7 (NM_000072.3) encodes the major glycoprotein of the platelet surface, which serves as a receptor for thrombospondin and is involved in cell adhesion /blood coagulation, shows frameshift variant in 5/12 alleles of APS group.

Conclusion:  We demonstrated high-throughput profiling of the genomic and transcriptomic data in APS patient group. Several novel, potentially disease-associated variants were identified. Further investigation regarding functional relationship with APS pathogenensis, and comparison between primary and secondary APS is needed.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/investigating-the-genetic-variations-of-antiphospholipid-syndrome-by-high-throughput-exome-sequencing/