Cardiology Genetics Report Long QT Syndrome (LQTS) Panel

Transcription

1 Patient Name: Test(s) Requested: The ordered test and the genes analyzed are Genes Evaluated (Disease): Result: Only mutations detected appear here KCNQ1 (LQT1 and Jervell and LangeNielsen syndrome), KCNH2 (LQT2), SCN5A (LQT3), ANK2 (LQT4), KCNE1 (LQT5 and Jervell and LangeNielsen syndrome), KCNE2 (LQT6), KCNJ2 (LQT7 and Andersen Tawil syndrome), CACNA1C (LQT8 and Timothy syndrome), CAV3 (LQT9), SCN4B (LQT10), AKAP9 (LQT11), SNTA1 (LQT12) POSITIVE Gene cdna Variant Zygosity Classification KCNQ1 c.1663 C>T p.arg555cys (R555C) Heterozygous Diseasecausing mutation No other diseasecausing mutations associated with LQTS were detected by sequence analysis of the 12 genes of the LQTS panel in this individual. Interpretation: Expands on the genetics This individual is heterozygous for a published missense mutation in the KCNQ1 gene, consistent with a genetic form of LQTS. Familial Long QT syndrome is primarily an autosomal dominant disease caused by mutation(s) in cardiac ion channel genes. Mutations in these genes tend to prolong the duration of the ventricular action potential, thus lengthening the QT interval seen on an ECG (Goldenberg I et al., 2008; Priori S et al., 2004). LQTS is associated with increased risk for syncope, ventricular arrhythmia and sudden cardiac death in young adults with normal heart structure (Vincent G, 1998). Mutations in the KCNQ1 gene have been reported in approximately 39%62% of patients with autosomal dominant long QT syndrome, and are associated with increased risk of cardiac events triggered by emotion, exercise and vigorous activity, particularly swimming (Priori S et al., 2004; Vincent G, 2009). KCNQ1 R555C p.arg555cys (R555C) CGC>TGC: c.1663 C>T in exon 13 of the KCNQ1 gene (NM_ ) The R555C mutation in KCNQ1 has been reported multiple times in association with LQTS, including one study that found this mutation was associated with druginduced symptoms and often borderline or no QT prolongation in three families with LQTS (Donger C et al., 1997; Park K et al., 2005; Kapplinger J et al., 2009). Functional studies report that R555C results in abnormal potassium channel function (Peroz D et al., 2008; Coyan F et al., 2014). This mutation was absent from >2,600 published control alleles (Kapplinger J et al., 2009), and the R555C mutation was not observed in approximately 6,500 samples from individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Located in the Cterminus of KCNQ1, R555C results in a nonconservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties (Park K et al., 2005). Other missense mutations affecting the same codon (R555H, R555S) as well as mutations in nearby codons (G548D, V554A, K557E, R562M) have also been observed in patients with LQTS, further supporting the functional importance of this residue and region of the protein (Stenson et al., 2014). In summary, R555C in the KCNQ1 gene is interpreted as a diseasecausing mutation. x 207 Perry Parkway Gaithersburg, MD Tel (301) Fax (301) Page 1 of 4

2 Patient Name: Outlines followup recommendations references to None management Providedguidelines, risks to family members Liz Butler or recommendations for genetic counseling. Recommendation: 1. It is recommended that this individual and any firstdegree relatives receive continued clinical evaluation and followup for LQTS. 2. Based on this genetic test result, targeted genetic testing is now available for this family, and is recommended for all of this patient's firstdegree relatives and other atrisk family members. Testing can identify family members at increased risk of developing LQTS based on the presence of the mutation. For this familial mutation, genetic testing of other family members only requires testing for this mutation, not the full LQTS panel. 3. Genetic counseling is recommended to discuss the implications of this test report, specifically the risk of recurrence for this family, and to provide testing for other atrisk family members. Methods: Describes the methodology used by the lab for that particular test. Using genomic DNA from the submitted specimen, the coding regions and splice junctions of the 12 genes (Only exons 144 for CACNA1C, only the KCNQ1binding domains including Ser1570 residue for AKAP9) were enriched by multiplex PCR and sequenced simultaneously by massively parallel (NextGen) sequencing on an Illumina HiSeq instrument with 1x50 pairedend reads. Bidirectional sequence was assembled, aligned to reference gene sequences based on human genome build GRCh37/UCSC hg19, and analyzed for sequence variants. Capillary sequencing was used to confirm all potentially pathogenic variants and to obtain sequence for regions where fewer than 15 reads were achieved by NextGen sequencing. Sequence alterations were reported according to the Human Genome Variation Society (HGVS) nomenclature guidelines. If present, apparently homozygous variants were confirmed using alternate primer pairs to significantly reduce the possibility of allele dropout. GeneDx 207 Perry Parkway Gaithersburg, MD Tel (301) Fax (301) Page 2 of 4

3 Patient Name: Supplemental Variant Information: Gene: cdna Variant (Protein) Classification Zygosity KCNQ1: c.1663 C>T p.arg555cys (R555C) Diseasecausing mutation Heterozygous Chr: Position 11: dbsnp 1000G 1000G_AMR 1000G_EAS 1000G_SAS 1000G_AFR 1000G_EUR 1000G_Highest 1000G_Highest_Sub ESP_EA ESP_AA ESP_Samples_Covered 6478 ESP_Avg_Rd_Depth 60.0 Sift PPH2 MutTaster_Score MutTaster_Pred rs (D) 1.0 (D) (D) D (D) Interpro_Domain Potassium channel, voltage dependent, KCNQ, Cterminal (1) ClinVar Pathogenic Provides evidence to support the variant in the attached result report This supplement provides evidence to support the classification of each reportable variant in the attached result report. This information is provided as a resource and may not be inclusive of all available information used by GeneDx for variant classification. The variant classification does not rely solely on any one of the individual criterion provided below. In addition, each criterion is weighted differently to derive the classification. This information is subject to change over time and may differ from what is currently available. This supplement is provided upon request to ordering providers. GeneDx has already conducted a thorough analysis of the data at the time testing was ordered and does not provide additional support to providers who have questions about the tools used in variant analysis and interpretation for a specific case. Results should always be interpreted in the context of the patient's clinical presentation. Note that the in silico scores used by GeneDx are precomputed and may change over time. In silico models use algorithms that predict the effect a variant may have on the protein, but they do not provide direct evidence regarding the actual impact on protein structure or function. The specificity of these models is typically low and they may produce discordant results (Flanagan 2010). In silico models should be interpreted with caution and only be used in combination with other available evidence to support the classification of any variant. Blank fields indicate that no data was available at time of analysis. For more information about the specific populations included in the 1000 Genomes Project, please see (McVean et al., 2012). For information about the populations included in the ESP data, please see The Exome Aggregation Consortium (ExAC) provides a betaversion of a set of exome sequencing data from a variety of largescale sequencing projects. A peerreviewed publication and final release of data are currently pending. The data includes low coverage and poor confidence calls which affect the data quality. The ExAC set includes data from individuals who were recruited for diseasespecific studies, including cancer and cardiovascular diseases. Therefore, GeneDx does not routinely consider data from the ExAC browser in variant interpretation at this time but will continue to evaluate the utility of this data set in a clinical setting and will include ExAC data once a peerreviewed publication is available and the full data set is released. REFERENCES: Genomes Project: McVean et al. (2012) Nature 491 (7422):5665 (PMID: ). 2. Exome Variant Server, NHLBI Exome Sequencing Project (ESP), Seattle, WA (URL: 3. SIFT: Kumar et al. (2009) Nature protocols 4 (7): (PMID: ) 4. Polyphen2: Adzhubei et al. (2010) Nature methods 7 (4):2489 (PMID: ) 5. Mutation Taster: Schwarz et al. (2014) Nature methods 11 (4):3612 (PMID: ) 6. SIFT and PolyPhen: Flanagan et al. (2010) Genet Test Mol Biomarkers Aug;14 (4):5337 (PMID ) 7. Interpro: Jones et al. (2014) Bioinformatics (Oxford, England) 30 (9): (PMID: ) 8. ClinVar: Landrum et al. (2014) Nucleic acids research 42 (Database issue):d9805 (PMID: ) GeneDx 207 Perry Parkway Gaithersburg, MD Tel (301) Fax (301) Page 3 of 4

4 Patient Name: Frequency/Catalog Information dbsnp NCBI repository for single base nucleotide substitutions and short deletion and insertion polymorphisms 1000G 1000 Genomes is a catalog of human genetic sequence variation obtained through genomic sequencing of 2500 individuals. Displayed valued indicates allelic frequency of the variant, with percent frequency displayed in parentheses. 1000G_AMR 1000G variant metafrequency percentage for individuals of American ancestry 1000G_EAS 1000G variant metafrequency percentage for individuals of East Asian ancestry 1000G_SAS 1000G variant metafrequency percentage for individuals of South Asian ancestry 1000G_AFR 1000G variant metafrequency percentage for individuals of African ancestry 1000G_EUR 1000G variant metafrequency percentage for individuals of European ancestry 1000G_Highest Highest reported percentage frequency of a variant in any 1000G subpopulation 1000G_Highest_Sub Subpopulation referenced in 1000G_Highest ESP_EA NHLBI Exome Sequencing Project (ESP) allelic frequency for individuals of European ancestry, including both healthy individuals and individuals from diseasespecific genetic studies ESP_AA NHLBI Exome Sequencing Project (ESP) allelic frequency for individuals of African ancestry, including both healthy individuals and individuals from diseasespecific genetic studies Information on Prediction Scores Sift Calculates the conservation of an amino acid and the protein tolerance to a proposed amino acid change. Scores range from 0 to 1 and are considered damaging if > PPH2 PolyPhen2 score predicts the probability that a variant is damaging using a machinelearning model and the HumDiv training dataset compiled from pathogenic variants known to cause human disorders. Scores range from 0 to 1: < 0.5 neutral, >= 0.5 possibly damaging, >= 0.9 damaging. MutTaster_Pred Predicts the effect of an amino acid variant. Predictions are: A Diseasecausing Automatic (known pathogenic), 'D' Diseasecausing, 'N' Polymorphism, P Polymorphism Automatic (known benign). MutTaster_Score Represents the strength of the calculated MutTaster_Pred matching a simple, automated prediction based on population statistics and ClinVar data (Example: A highscoring variant may be both calculated to be damaging and has a 'damaging' flag in ClinVar.) A high score does NOT indicate a high probability of accuracy. Interpro_Domain Domain in conserved site on which the variant is located. Domain annotations come from the Interpro database. The number in parentheses reflects how many times Interpro has assigned the variant position to that domain, typically derived from different predicting databases. ClinVar Classification of variant in ClinVar database, an NCBI archive of human variants with supporting evidence of phenotypic association. Report electronically signed by: Report electronically signed by: Sequence changes in the coding regions of KCNQ1, KCNH2, and SCN5A which are not known to definitively cause LQTS or a related arrhythmia: KCNH2, c.2690 A>C, p.lys897thr (K897T), Heterozygous; SCN5A, c.1673 A>G, p.his558arg (H558R), Homozygous References: Goldenberg et al. (2008) Current problems in cardiology 33 (11):62994 (PMID: ); Priori et al. (2004) Annals of the New York Academy of Sciences 1015 :96110 (PMID: ); Vincent et al. (1998) Annual review of medicine 49 :26374 (PMID: ); Vincent G. (Updated [4/2009]). RomanoWard Syndrome. In: GeneReviews at GeneTests Medical Genetics Information Resource (database online). Copyright, University of Washington, Seattle Available at Accessed [4/2012]; Donger C et al. KVLQT1 CTerminal Missense Mutation Causes a Forme Fruste LongQT Syndrome. Circulation. 96: , 1997; Park K et al. Impaired KCNQ1KCNE1 and phosphatidylinositol4,5bisphosphate interaction underlies the long QT syndrome. Circ Res. 96:730739, 2005; Kapplinger J et al., Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. Heart Rhythm. 6: , 2009; Peroz D et al. Kv7.1 (KCNQ1) properties and channelopathies. J Physiol 586.7: , 2008; Coyan et al. (2014) PloS one 9 (3):e93255; Exome Variant Server, NHLBI Exome Sequencing Project (ESP), Seattle, WA (URL: [12/2014]; Stenson et al. (2014) Human genetics 133 (1):19 (PMID: ) For additional information about this test result, please see attached brochure or visit the GeneDx website: cardiology/ Limitations: Genetic testing using the methods applied at GeneDx is expected to be highly accurate. Normal findings do not rule out the diagnosis of a genetic disorder since some genetic abnormalities may be undetectable with this test. This sequencing test cannot reliably detect mosaicism. Some genes have inherent sequence properties (for example: repeat, homology, or pseudogene regions, high GC content, rare polymorphisms) that may result in suboptimal data, and mutations in those regions may not be reliably identified. False negative results may also occur in the setting of bone marrow transplantation, recent blood transfusion, or suboptimal DNA quality. The chance of a false positive or false negative result due to laboratory errors incurred during any phase of testing cannot be completely excluded. Interpretations are made with the assumption that any information provided on family relationships is accurate. Consultation with a genetics professional is recommended for interpretation of results. Disclaimer: This test was developed and its performance characteristics determined by GeneDx. It has not been cleared or approved by the U.S. Food and Drug Administration. The laboratory is regulated under CLIA as qualified to perform highcomplexity testing. This test is used for clinical purposes. It should not be regarded as investigational or for research. GeneDx 207 Perry Parkway Gaithersburg, MD Tel (301) Fax (301) Page 4 of 4

5 Patient Name: GeneDx Accession No: Date Specimen Obtained: Date Specimen Received: Date Test(s) Started: Date of Report: XXXXXXX 3/9/2015 3/10/2015 3/10/2015 4/3/2015 Image displays the location of the genetic alteration along the ion channel Heterozygous R555C in KCNQ1 Modified From Original Image: Inherited Arrhythmias Database This assay was developed and its performance determined by GeneDx for the sole purpose of identifying small sequence variants in the gene(s) tested. As with any genetic testing assay, this test does not detect large chromosomal aberrations, such as larger deletions and duplications (larger than 5bp) or rearrangements. Normal findings do not rule out the diagnosis of any disorder since some genetic abnormalities may be undetectable with this assay. Clinical implications of some variations may be unknown at the time of this report. This test should be used for clinical purposes only. It has not been cleared or approved by the FDA. The FDA has determined that such clearance or approval is not necessary. Pursuant to the requirements of CLIA '88, this laboratory has established and verified the test's accuracy and precision. CLIA ID#: 21D MD License: 953. GeneDx 207 Perry Parkway Gaithersburg, MD Tel (301) Fax (301)