Targeted deep sequencing reveals no definitive evidence for somatic mosaicism in atrial fibrillation

Jason D. Roberts, James Longoria, Annie Poon, Michael H. Gollob, Thomas Dewland, Pui Yan Kwok, Jeffrey E. Olgin, Rahul C. Deo, Gregory M. Marcus

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Background - Studies of ≤15 atrial fibrillation (AF) patients have identified atrial-specific mutations within connexin genes, suggesting that somatic mutations may account for sporadic cases of the arrhythmia. We sought to identify atrial somatic mutations among patients with and without AF using targeted deep next-generation sequencing of 560 genes, including genetic culprits implicated in AF, the Mendelian cardiomyopathies and channelopathies, and all ion channels within the genome. Methods and Results - Targeted gene capture and next-generation sequencing were performed on DNA from lymphocytes and left atrial appendages of 34 patients (25 with AF). Twenty AF patients had undergone cardiac surgery exclusively for pulmonary vein isolation and 17 had no structural heart disease. Sequence alignment and variant calling were performed for each atrial-lymphocyte pair using the Burrows-Wheeler Aligner, the Genome Analysis Toolkit, and MuTect packages. Next-generation sequencing yielded a median 265-fold coverage depth (interquartile range, 64-369). Comparison of the 3 million base pairs from each atrial-lymphocyte pair revealed a single potential somatic missense mutation in 3 AF patients and 2 in a single control (12 versus 11%; P=1). All potential discordant variants had low allelic fractions (range, 2.3%-7.3%) and none were detected with conventional sequencing. Conclusions - Using high-depth next-generation sequencing and state-of-the art somatic mutation calling approaches, no pathogenic atrial somatic mutations could be confirmed among 25 AF patients in a comprehensive cardiac arrhythmia genetic panel. These findings indicate that atrial-specific mutations are rare and that somatic mosaicism is unlikely to exert a prominent role in AF pathogenesis.

Original languageEnglish (US)
Pages (from-to)50-57
Number of pages8
JournalCirculation: Cardiovascular Genetics
Volume8
Issue number1
DOIs
StatePublished - Feb 4 2015
Externally publishedYes

Fingerprint

High-Throughput Nucleotide Sequencing
Mosaicism
Atrial Fibrillation
Mutation
Lymphocytes
Cardiac Arrhythmias
Channelopathies
Genome
Genes
Atrial Appendage
Connexins
Pulmonary Veins
Sequence Alignment
Missense Mutation
Cardiomyopathies
Ion Channels
Base Pairing
Thoracic Surgery
Heart Diseases
DNA

Keywords

  • Arrhythmias, cardiac
  • Atrial fibrillation
  • Cardiac electrophysiology
  • Computational biology
  • Genetics
  • Mosaicism

ASJC Scopus subject areas

  • Cardiology and Cardiovascular Medicine
  • Genetics(clinical)
  • Genetics

Cite this

Targeted deep sequencing reveals no definitive evidence for somatic mosaicism in atrial fibrillation. / Roberts, Jason D.; Longoria, James; Poon, Annie; Gollob, Michael H.; Dewland, Thomas; Kwok, Pui Yan; Olgin, Jeffrey E.; Deo, Rahul C.; Marcus, Gregory M.

In: Circulation: Cardiovascular Genetics, Vol. 8, No. 1, 04.02.2015, p. 50-57.

Research output: Contribution to journalArticle

Roberts, Jason D. ; Longoria, James ; Poon, Annie ; Gollob, Michael H. ; Dewland, Thomas ; Kwok, Pui Yan ; Olgin, Jeffrey E. ; Deo, Rahul C. ; Marcus, Gregory M. / Targeted deep sequencing reveals no definitive evidence for somatic mosaicism in atrial fibrillation. In: Circulation: Cardiovascular Genetics. 2015 ; Vol. 8, No. 1. pp. 50-57.
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abstract = "Background - Studies of ≤15 atrial fibrillation (AF) patients have identified atrial-specific mutations within connexin genes, suggesting that somatic mutations may account for sporadic cases of the arrhythmia. We sought to identify atrial somatic mutations among patients with and without AF using targeted deep next-generation sequencing of 560 genes, including genetic culprits implicated in AF, the Mendelian cardiomyopathies and channelopathies, and all ion channels within the genome. Methods and Results - Targeted gene capture and next-generation sequencing were performed on DNA from lymphocytes and left atrial appendages of 34 patients (25 with AF). Twenty AF patients had undergone cardiac surgery exclusively for pulmonary vein isolation and 17 had no structural heart disease. Sequence alignment and variant calling were performed for each atrial-lymphocyte pair using the Burrows-Wheeler Aligner, the Genome Analysis Toolkit, and MuTect packages. Next-generation sequencing yielded a median 265-fold coverage depth (interquartile range, 64-369). Comparison of the 3 million base pairs from each atrial-lymphocyte pair revealed a single potential somatic missense mutation in 3 AF patients and 2 in a single control (12 versus 11{\%}; P=1). All potential discordant variants had low allelic fractions (range, 2.3{\%}-7.3{\%}) and none were detected with conventional sequencing. Conclusions - Using high-depth next-generation sequencing and state-of-the art somatic mutation calling approaches, no pathogenic atrial somatic mutations could be confirmed among 25 AF patients in a comprehensive cardiac arrhythmia genetic panel. These findings indicate that atrial-specific mutations are rare and that somatic mosaicism is unlikely to exert a prominent role in AF pathogenesis.",
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AU - Kwok, Pui Yan

AU - Olgin, Jeffrey E.

AU - Deo, Rahul C.

AU - Marcus, Gregory M.

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N2 - Background - Studies of ≤15 atrial fibrillation (AF) patients have identified atrial-specific mutations within connexin genes, suggesting that somatic mutations may account for sporadic cases of the arrhythmia. We sought to identify atrial somatic mutations among patients with and without AF using targeted deep next-generation sequencing of 560 genes, including genetic culprits implicated in AF, the Mendelian cardiomyopathies and channelopathies, and all ion channels within the genome. Methods and Results - Targeted gene capture and next-generation sequencing were performed on DNA from lymphocytes and left atrial appendages of 34 patients (25 with AF). Twenty AF patients had undergone cardiac surgery exclusively for pulmonary vein isolation and 17 had no structural heart disease. Sequence alignment and variant calling were performed for each atrial-lymphocyte pair using the Burrows-Wheeler Aligner, the Genome Analysis Toolkit, and MuTect packages. Next-generation sequencing yielded a median 265-fold coverage depth (interquartile range, 64-369). Comparison of the 3 million base pairs from each atrial-lymphocyte pair revealed a single potential somatic missense mutation in 3 AF patients and 2 in a single control (12 versus 11%; P=1). All potential discordant variants had low allelic fractions (range, 2.3%-7.3%) and none were detected with conventional sequencing. Conclusions - Using high-depth next-generation sequencing and state-of-the art somatic mutation calling approaches, no pathogenic atrial somatic mutations could be confirmed among 25 AF patients in a comprehensive cardiac arrhythmia genetic panel. These findings indicate that atrial-specific mutations are rare and that somatic mosaicism is unlikely to exert a prominent role in AF pathogenesis.

AB - Background - Studies of ≤15 atrial fibrillation (AF) patients have identified atrial-specific mutations within connexin genes, suggesting that somatic mutations may account for sporadic cases of the arrhythmia. We sought to identify atrial somatic mutations among patients with and without AF using targeted deep next-generation sequencing of 560 genes, including genetic culprits implicated in AF, the Mendelian cardiomyopathies and channelopathies, and all ion channels within the genome. Methods and Results - Targeted gene capture and next-generation sequencing were performed on DNA from lymphocytes and left atrial appendages of 34 patients (25 with AF). Twenty AF patients had undergone cardiac surgery exclusively for pulmonary vein isolation and 17 had no structural heart disease. Sequence alignment and variant calling were performed for each atrial-lymphocyte pair using the Burrows-Wheeler Aligner, the Genome Analysis Toolkit, and MuTect packages. Next-generation sequencing yielded a median 265-fold coverage depth (interquartile range, 64-369). Comparison of the 3 million base pairs from each atrial-lymphocyte pair revealed a single potential somatic missense mutation in 3 AF patients and 2 in a single control (12 versus 11%; P=1). All potential discordant variants had low allelic fractions (range, 2.3%-7.3%) and none were detected with conventional sequencing. Conclusions - Using high-depth next-generation sequencing and state-of-the art somatic mutation calling approaches, no pathogenic atrial somatic mutations could be confirmed among 25 AF patients in a comprehensive cardiac arrhythmia genetic panel. These findings indicate that atrial-specific mutations are rare and that somatic mosaicism is unlikely to exert a prominent role in AF pathogenesis.

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