Ataxia-Telangiectasia

Ataxia-telangiectasia is an autosomal recessive neurogenetic condition characterized by progressive cerebellar ataxia, telangiectasias, and an increased risk for a variety of cancers in childhood. Carriers have an increased risk to develop cancer in adulthood.

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Test Code: 5600 Test Name: ATM specific site analysis TAT 7-14 days Gene: 1
Test Code: 5604 Test Name: ATM del/dup TAT 7-14 days Gene: 1
Test Code: 9014 Test Name: ATM seq and del/dup TAT 14-21 days Gene: 1

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Mutation Detection Rate

This test detects >99.9% of sequencing mutations in ATM, when present (analytic sensitivity).

Test Description

ATM coding exons 1-62 and well into the 5’ and 3’ ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis determines gene copy number for coding exons 1-62. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using 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). 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. Gross deletion/duplication analysis of ATM using read-depth from NGS data is also performed. Any copy number changes detected by NGS are confirmed by targeted chromosomal microarray and/or multiplex ligation-dependent probe amplification (MLPA).

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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