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Methodology

Methodology

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Molecular Genetics
DDeletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
  • Other
CSequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
  • Illumina NovaSeq 6000

Test development

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Test developed by laboratory (no manufacturer test name)

Test procedure

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Next-generation sequencing (NGS) and/or Sanger sequencing are performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for deletions/insertions (delins) less than 40 base pairs (bp), and above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed. There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences.(Unpublished Mayo method) See Targeted Genes and Methodology Details for Primary Hemophagocytic Lymphohistiocytosis (HLH) Gene Panel for details regarding the targeted genes analyzed for each test and specific gene regions not routinely covered. Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria. Genes analyzed: ADA, AP3B1, AP3D1, BLOC1S6, CD27, CD70, CDC42, CORO1A, CTPS1, IFNAR2, ITK, LYST, MAGT1, MVK, NLRC4, PRF1, RAB27A, SH2D1A, SLC7A7, STX11, STXBP2, UNC13D, and XIAP

Citations

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