Case Study – CES

24-05-2019

Clinical Exome Sequencing

Introductions:

Diagnostic odyssey caused due a negative clinical exome

result in a patient with high suspicion of a genetic condition
can cause frustration for families and physicians alike. In
addition, families experience anxiety due to the time taken
for next generation sequencing and high costs associated
with the test. Utilizing advanced analytical tools and well
curated databases can improve identification of variants. We
demonstrate that in cases with high suspicion of a genetic
condition identification of variants in a suspected gene can Name – Proband X
provide greater insight to physicians and improve accuracy
Age – 02 years
of diagnosis at comparatively lesser time.
Gender – Male
Proband profile:
Recommended Test – LifeCell
CES
A 2 year-old male presented with clinical indications
febrile seizures (multiple types seizures). A positive family
history of febrile seizure was reported. Proband was Previous genetic investigations,
if any – None
suspected to have Dravet Syndrome.
CES Reports – Heterozygous
VoUS variant reported in SCNLA
gene
Initial results of sequencing:

Targeted sequencing of SCN1A gene was performed at an outsourced lab M. The coverage of
the SCN1A gene was 100% in this assay. No pathogenic or likely pathogenic variant was
identified in this gene.
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Secondary analysis at LifeCell:

A secondary analysis was performed in-house. A heterozygous deep intronic variant (c.603-
91G>G/A) in intron 4 of SCN1A gene was identified. The observed variant has a minor
allele frequency of 0.47% in the 1000 Genomes database. The A allele has been previously
shown to disrupt the 5’ splice donor site of neonatal copy of exon 5 (5N), which drastically
reduces the expression of this exon relative to adult exon 5A. This variant was previously
reported as a risk factor for febrile seizures.

Genetic Counseling Recommendations:

 Validation of the variant by Sanger sequencing was recommended.

 Testing for the variant in the parents and other affected, unaffected members can help
further identify clinical significance

How is our analysis different?

Commonly, mutations in the exonic region that affect the protein function are associated with
clinical manifestations. However, evidence suggests that mutations that affect splicing can be
present in exonic, intronic or splice junctions. Such mutations can also be found in deep intronic
regions, many of which have been identified to be pathogenic. For this reason, at LifeCell we
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utilise advanced NGS data analysis software Golden Helix that allows identification of splice
site predictions for exonic and intronic variants not near splice sites. This can help uncover
variants in intronic regions. In addition, VarSeq which is an integrated software provides a
filtering and annotation engine to sift through large variant data sets. The analysis pipeline
automates workflow and analysis of variants for gene panels, exomes, and whole genomes.
Further, it provides access to a wide selection of public databases which Golden Helix curates
and updates on a quarterly basis. Updated data will ensure timely and accurate classification of
variants as new data is published in literature.

References:

Tate SK, Depondt C, Sisodiya SM, Cavalleri GL, Schorge S, Soranzo N, Thom M, Sen A, Shorvon SD, Sander
JW, Wood NW, Goldstein DB. Genetic predictors of the maximum doses patients receive during clinical use of
the anti-epileptic drugs carbamazepine and phenytoin. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5507-12.
Epub 2005 Apr 1.

Heinzen EL, Yoon W, Tate SK, Sen A, Wood NW, Sisodiya SM, Goldstein DB. Nova2 interacts with a cis-acting
polymorphism to influence the proportions of drug-responsive splice variants of SCN1A. Am J Hum Genet. 2007
May;80(5):876-83. Epub 2007 Apr 3.

Schlachter K, Gruber-Sedlmayr U, Stogmann E, Lausecker M, Hotzy C, Balzar J, Schuh E, Baumgartner C,

Mueller JC, Illig T, Wichmann HE, Lichtner P, Meitinger T, Strom TM, Zimprich A, Zimprich F. A splice site
variant in the sodium channel gene SCN1A confers risk of febrile seizures. Neurology. 2009 Mar 17;72(11):974-
8.
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