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Identification of Genetic Alterations, as Causative Genetic Defects in Long QT Syndrome, Using Next Generation Sequencing Technology.

Campuzano O, Sarquella-Brugada G, Mademont-Soler I, Allegue C, Cesar S, Ferrer-Costa C, Coll M, Mates J, Iglesias A, Brugada J, Brugada R - PLoS ONE (2014)

Bottom Line: Despite that several genes have been associated with the disease, nearly 20% of cases remain without an identified genetic cause.Both variants were confirmed by alternative techniques.Clinical and familiar correlation is crucial to elucidate the role of genetic variants identified to distinguish the pathogenic ones from genetic noise.

View Article: PubMed Central - PubMed

Affiliation: Cardiovascular Genetics Center, University of Girona-IdIBGi, Girona, Spain.

ABSTRACT

Background: Long QT Syndrome is an inherited channelopathy leading to sudden cardiac death due to ventricular arrhythmias. Despite that several genes have been associated with the disease, nearly 20% of cases remain without an identified genetic cause. Other genetic alterations such as copy number variations have been recently related to Long QT Syndrome. Our aim was to take advantage of current genetic technologies in a family affected by Long QT Syndrome in order to identify the cause of the disease.

Methods: Complete clinical evaluation was performed in all family members. In the index case, a Next Generation Sequencing custom-built panel, including 55 sudden cardiac death-related genes, was used both for detection of sequence and copy number variants. Next Generation Sequencing variants were confirmed by Sanger method. Copy number variations variants were confirmed by Multiplex Ligation dependent Probe Amplification method and at the mRNA level. Confirmed variants and copy number variations identified in the index case were also analyzed in relatives.

Results: In the index case, Next Generation Sequencing revealed a novel variant in TTN and a large deletion in KCNQ1, involving exons 7 and 8. Both variants were confirmed by alternative techniques. The mother and the brother of the index case were also affected by Long QT Syndrome, and family cosegregation was observed for the KCNQ1 deletion, but not for the TTN variant.

Conclusions: Next Generation Sequencing technology allows a comprehensive genetic analysis of arrhythmogenic diseases. We report a copy number variation identified using Next Generation Sequencing analysis in Long QT Syndrome. Clinical and familiar correlation is crucial to elucidate the role of genetic variants identified to distinguish the pathogenic ones from genetic noise.

No MeSH data available.


Related in: MedlinePlus

Pedigree and electropherogram.(A) Index case is II.1. White round/squares indicate healthy status after clinical evaluation. Grey round/squares indicate LQTS after clinical evaluation. Plus sign indicates carrier of genetic variation. Minus sign indicates non-carrier of the genetic variation. (B) Electropherogram of the genetic variation identified (p.R20729G_TTN).
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pone-0114894-g002: Pedigree and electropherogram.(A) Index case is II.1. White round/squares indicate healthy status after clinical evaluation. Grey round/squares indicate LQTS after clinical evaluation. Plus sign indicates carrier of genetic variation. Minus sign indicates non-carrier of the genetic variation. (B) Electropherogram of the genetic variation identified (p.R20729G_TTN).

Mentions: We analyzed 55 genes previously associated with SCD (Table 1). After the NGS process and the application of bioinformatics pipeline, the call rate ranged from 99,6% to 98,92% at 20x and 100x respectively in this sample. We selected the Non Synonymous (NS) variants with a MAF<1% in the EVS for its conventional Sanger sequencing confirmation. Only one single nucleotide variant (SNV) was confirmed in the index case, the TTN gene (p.R20729G). This novel variant is consequence of a nucleotide change of A to G (c.62185A>G). The genetic variation was not previously identified in locus specific databases, considered therefore a novel GVUS. It was predicted in silico as pathogenic in all databases consulted. In addition, alignment between species showed a high level of conservation. However, family segregation showed that only the index case’s father carried the same genetic variation (Fig. 2).


Identification of Genetic Alterations, as Causative Genetic Defects in Long QT Syndrome, Using Next Generation Sequencing Technology.

Campuzano O, Sarquella-Brugada G, Mademont-Soler I, Allegue C, Cesar S, Ferrer-Costa C, Coll M, Mates J, Iglesias A, Brugada J, Brugada R - PLoS ONE (2014)

Pedigree and electropherogram.(A) Index case is II.1. White round/squares indicate healthy status after clinical evaluation. Grey round/squares indicate LQTS after clinical evaluation. Plus sign indicates carrier of genetic variation. Minus sign indicates non-carrier of the genetic variation. (B) Electropherogram of the genetic variation identified (p.R20729G_TTN).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4262446&req=5

pone-0114894-g002: Pedigree and electropherogram.(A) Index case is II.1. White round/squares indicate healthy status after clinical evaluation. Grey round/squares indicate LQTS after clinical evaluation. Plus sign indicates carrier of genetic variation. Minus sign indicates non-carrier of the genetic variation. (B) Electropherogram of the genetic variation identified (p.R20729G_TTN).
Mentions: We analyzed 55 genes previously associated with SCD (Table 1). After the NGS process and the application of bioinformatics pipeline, the call rate ranged from 99,6% to 98,92% at 20x and 100x respectively in this sample. We selected the Non Synonymous (NS) variants with a MAF<1% in the EVS for its conventional Sanger sequencing confirmation. Only one single nucleotide variant (SNV) was confirmed in the index case, the TTN gene (p.R20729G). This novel variant is consequence of a nucleotide change of A to G (c.62185A>G). The genetic variation was not previously identified in locus specific databases, considered therefore a novel GVUS. It was predicted in silico as pathogenic in all databases consulted. In addition, alignment between species showed a high level of conservation. However, family segregation showed that only the index case’s father carried the same genetic variation (Fig. 2).

Bottom Line: Despite that several genes have been associated with the disease, nearly 20% of cases remain without an identified genetic cause.Both variants were confirmed by alternative techniques.Clinical and familiar correlation is crucial to elucidate the role of genetic variants identified to distinguish the pathogenic ones from genetic noise.

View Article: PubMed Central - PubMed

Affiliation: Cardiovascular Genetics Center, University of Girona-IdIBGi, Girona, Spain.

ABSTRACT

Background: Long QT Syndrome is an inherited channelopathy leading to sudden cardiac death due to ventricular arrhythmias. Despite that several genes have been associated with the disease, nearly 20% of cases remain without an identified genetic cause. Other genetic alterations such as copy number variations have been recently related to Long QT Syndrome. Our aim was to take advantage of current genetic technologies in a family affected by Long QT Syndrome in order to identify the cause of the disease.

Methods: Complete clinical evaluation was performed in all family members. In the index case, a Next Generation Sequencing custom-built panel, including 55 sudden cardiac death-related genes, was used both for detection of sequence and copy number variants. Next Generation Sequencing variants were confirmed by Sanger method. Copy number variations variants were confirmed by Multiplex Ligation dependent Probe Amplification method and at the mRNA level. Confirmed variants and copy number variations identified in the index case were also analyzed in relatives.

Results: In the index case, Next Generation Sequencing revealed a novel variant in TTN and a large deletion in KCNQ1, involving exons 7 and 8. Both variants were confirmed by alternative techniques. The mother and the brother of the index case were also affected by Long QT Syndrome, and family cosegregation was observed for the KCNQ1 deletion, but not for the TTN variant.

Conclusions: Next Generation Sequencing technology allows a comprehensive genetic analysis of arrhythmogenic diseases. We report a copy number variation identified using Next Generation Sequencing analysis in Long QT Syndrome. Clinical and familiar correlation is crucial to elucidate the role of genetic variants identified to distinguish the pathogenic ones from genetic noise.

No MeSH data available.


Related in: MedlinePlus