Next-generation sequencing of nine atrial fibrillation candidate genes identified novel de novo mutations in patients with extreme trait of atrial fibrillation.
BACKGROUND
Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. Genome-wide association studies (GWAS) have identified common variants in nine genomic regions associated with AF (KCNN3, PRRX1, PITX2, WNT8A, CAV1, C9orf3, SYNE2, HCN4 and ZFHX3 genes); however, the genetic variability of these risk variants does not explain the entire genetic susceptibility to AF. Rare variants missed by GWAS may also contribute to genetic risk of AF.


METHODS
We used an extreme trait design to sequence carefully selected probands with extreme phenotypes and their unaffected parents to identify rare de novo variants or mutations. Based on the hypothesis that common and rare variants may colocate in the same disease susceptibility gene, we used next-generation sequencing to sequence these nine published AF susceptibility genes identified by GWAS (a total of 179 exons) in 20 trios, 200 unrelated patients with AF and 200 non-AF controls.


RESULTS
We identified a novel mutation in the 5' untranslated region of the PITX2 gene, which localised in the transcriptionally active enhancer region. We also identified one missense exon mutation in KCNN3, two in ZFHX3 and one in SYNE2. None of these mutations were present in other unrelated patients with AF, healthy controls, unaffected parents and are thus novel and de novo (p<10(-4)). Functional study showed that the mutation in the 5' untranslated region of the PITX2 gene significantly downregulated PITX2 expression in atrial myocytes, either in basal condition or during rapid pacing. In silico analysis showed that the missense mutation in ZFHX3 results in damage of the ZFHX3 protein structure.


CONCLUSIONS
The genetic architecture of subjects with extreme phenotypes of AF is similar to that of rare or Mendelian diseases, and mutations may be the underlying cause.
Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin, Taiwan Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
Chia-Ti
CT
Tsai
Genome and Systems Biology Degree Program, Department of Life Science, National Taiwan University, Taipei, Taiwan Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan.
Chia-Shan
CS
Hsieh
Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin, Taiwan.
Sheng-Nan
SN
Chang
Genome and Systems Biology Degree Program, Department of Life Science, National Taiwan University, Taipei, Taiwan Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan.
Eric Y
EY
Chuang
Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan.
Jyh-Ming Jimmy
JM
Juang
Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan.
Lian-Yu
LY
Lin
Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan.
Ling-Ping
LP
Lai
Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan.
Juey-Jen
JJ
Hwang
Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan Department of Laboratory Medicine, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan.
Fu-Tien
FT
Chiang
Division of Cardiology, Department of Internal Medicine, National Taiwan University College of Medicine and Hospital, Taipei, Taiwan.
Jiunn-Lee
JL
Lin
D020121:5' Untranslated Regions / Q000235:genetics; D001281:Atrial Fibrillation / Q000235:genetics* / Q000473:pathology*; D001483:Base Sequence; D005091:Exons / Q000235:genetics; D056726:Genetic Association Studies / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D008840:Microfilament Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D010641:Phenotype; D011487:Protein Conformation; D051640:Small-Conductance Calcium-Activated Potassium Channels / Q000235:genetics; D018709:Statistics, Nonparametric; D014157:Transcription Factors / Q000235:genetics*; D000097577:Homeobox Protein PITX2
D020121:5' Untranslated Regions; D018398:Homeodomain Proteins; D008840:Microfilament Proteins; D009419:Nerve Tissue Proteins; D009687:Nuclear Proteins; D051640:Small-Conductance Calcium-Activated Potassium Channels; D014157:Transcription Factors; D000097577:Homeobox Protein PITX2; C406328:KCNN3 protein, human; C485904:SYNE2 protein, human; C071660:ZFHX3 protein, human
Arrhythmias; Genetic screening/counselling; Genetics