NCLNext

The neuronal ceroid lipofuscinoses (NCLs) are a group of neurodegenerative, lysosomal storage disorders characterized by seizures, progressive cognitive and motor impairment, and vision loss. Also known as Batten disease, there are 14 types of NCL that have significant clinical overlap; genetic testing is often necessary to distinguish between them.

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Test Code: 7025 Test Name: NCLNext TAT 4-6 weeks Genes: 13
Test Code: 7050 Test Name: PPT1 seq and del/dup TAT 2-4 weeks Gene: 1
Test Code: 7051 Test Name: TPP1 seq and del/dup TAT 2-4 weeks Gene: 1
Test Code: 7052 Test Name: CTSD seq and del/dup TAT 2-4 weeks Gene: 1
Test Code: 7054 Test Name: CLN3 seq and del/dup TAT 2-4 weeks Gene: 1

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Mutation Detection Rate

NCLNext and single gene testing for PPT1, TPP1, CLN3, and CTSD can detect >99.9% of described mutations in the included gene(s), when present (analytic sensitivity).

Test Description

NCLNext includes 13 genes known to be associated with the NCLs: ATP13A2, CLN3, CLN5, CLN6, CLN8, CTSD, CTSF, DNAJC5, GRN, KCTD7, MFSD8, PPT1, and TPP1. These genes are also included in our progressive myoclonus epilepsy panel (PMENext) and comprehensive epilepsy panel (EpilepsyNext). Single gene testing is available for PPT1, TPP1, CLN3, and CTSD. Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using a standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology using long biotinylated oligonucleotide probes, followed by polymerase chain reaction (PCR) and next generation sequencing (NGS).

Additional Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing.This assay targets all coding domains, and well into the flanking 5’ and 3’ ends of all the introns and untranslated regions. Gross deletion/duplication analysis for available genes is performed utilizing a targeted chromosomal microarray. Specific mutation analysis is also available for individual mutations in genes on NCLNext that are known to be in the family.

 

1. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932.

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