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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

MLPA capillary electrophoresis pattern.(A) index case and (B) her healthy father, both analysed with SALSA MLPA probemix P114-B2 Long QT. Comparing both profiles, the patient’s deletion of exons 7 and 8 of the KCNQ1 gene can be appreciated.
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pone-0114894-g004: MLPA capillary electrophoresis pattern.(A) index case and (B) her healthy father, both analysed with SALSA MLPA probemix P114-B2 Long QT. Comparing both profiles, the patient’s deletion of exons 7 and 8 of the KCNQ1 gene can be appreciated.

Mentions: On the other hand, NGS analysis revealed a deletion of exons 7 and 8 in the KCNQ1 gene (Fig. 3). The raw coverage normalization showed that pooled samples were comparable in terms of coverage and no major biases between samples were found (average normalized coverage is 6.7 with sd 0.11 yielding a cv of 1.7%; average sd of normalized coverage is.60 with sd 0.02 yielding a cv of 4.1%). Then, the analysis of corrected log2 ratio coverage by genomic position for each sample was performed. The corrected log2 ratios fit a Gaussian distribution. A baseline from all pool was inferred and each sample was compared with this prediction. The deviated exons from this baseline were labelled as duplications or deletions. The analysis showed an intense signal over these two exons with more than 6 standard deviations from the mean (log2 mean ratio for this signal is −1,1±0,09 sd). This CNV alteration was confirmed by MLPA (Fig. 4). Family segregation studies revealed that the brother and the mother of the proband (both affected by LQTS) shared the same CNV, while the father’s MLPA pattern was normal. The deletion of exons 7 and 8 of KCNQ1 was also confirmed in the brother and the mother of the proband at the mRNA level (Fig. 5).


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)

MLPA capillary electrophoresis pattern.(A) index case and (B) her healthy father, both analysed with SALSA MLPA probemix P114-B2 Long QT. Comparing both profiles, the patient’s deletion of exons 7 and 8 of the KCNQ1 gene can be appreciated.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0114894-g004: MLPA capillary electrophoresis pattern.(A) index case and (B) her healthy father, both analysed with SALSA MLPA probemix P114-B2 Long QT. Comparing both profiles, the patient’s deletion of exons 7 and 8 of the KCNQ1 gene can be appreciated.
Mentions: On the other hand, NGS analysis revealed a deletion of exons 7 and 8 in the KCNQ1 gene (Fig. 3). The raw coverage normalization showed that pooled samples were comparable in terms of coverage and no major biases between samples were found (average normalized coverage is 6.7 with sd 0.11 yielding a cv of 1.7%; average sd of normalized coverage is.60 with sd 0.02 yielding a cv of 4.1%). Then, the analysis of corrected log2 ratio coverage by genomic position for each sample was performed. The corrected log2 ratios fit a Gaussian distribution. A baseline from all pool was inferred and each sample was compared with this prediction. The deviated exons from this baseline were labelled as duplications or deletions. The analysis showed an intense signal over these two exons with more than 6 standard deviations from the mean (log2 mean ratio for this signal is −1,1±0,09 sd). This CNV alteration was confirmed by MLPA (Fig. 4). Family segregation studies revealed that the brother and the mother of the proband (both affected by LQTS) shared the same CNV, while the father’s MLPA pattern was normal. The deletion of exons 7 and 8 of KCNQ1 was also confirmed in the brother and the mother of the proband at the mRNA level (Fig. 5).

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